Single particle cryo-EM reconstruction of 52 kDa streptavidin at three.2 Angstrom decision

Preparation of frozen-hydrated SA specimen on graphene movie

On this research, we used a single-crystalline monolayer graphene over a Quantifoil R0.6/1 gold grid because the supporting movie to facilitate the cryogenic SA specimen preparation (see Strategies for extra particulars). Utilizing a modified model of our earlier imaging technique to mix the Cs-corrector and VPP for cryo-EM, we had been capable of gather high-resolution datasets of vitrified SA specimens with excessive effectivity (Strategies). When examined below the VPP-Cs-corrector-coupled Titan Krios at 300 kV with section shift starting from 30° to 120°, the SA specimens demonstrated monodisperse particles with a excessive distinction that may very well be simply recognized and picked utilizing automated algorithms (Fig. 1a). We discovered that the single-crystalline graphene with a monolayer of carbon atoms launched very low background noise to the specimen and will additionally function an excellent reference for the evaluation of the cryo-EM picture high quality and movement correction with its hexagonal lattice sign24,25,26. After the movement correction of the uncooked film stacks of the specimen, we calculated the Fourier remodel of the motion-corrected micrographs. In micrographs with good high quality, we noticed clear reflection spots at 2.13 Å decision in a hexagonal sample equivalent to the graphene lattice at its first order (Supplementary Fig. 1), indicating a profitable movement correction with high-resolution info recovered to not less than 2.13 Å. It’s value noting that these reflection spots weren’t clear or sharp sufficient with out the correct movement correction (Supplementary Fig. 1). Subsequently, the sharpness of the reflection spots of single-crystalline graphene within the Fourier remodel can function an excellent indicator to guage the standard of the micrographs and the motion-correction effectivity. We additionally examined the Fourier transforms of varied areas on the identical specimen grid and located that almost all of them demonstrated a constantly hexagonal lattice diffraction sample in the identical orientation, indicating the presence of a single-crystalline graphene movie over the grid (Supplementary Fig. 1D).

Fig. 1figure1

The SPA cryo-EM of SA. a A consultant micrograph of the SA specimen by the VPP-Cs-corrector-coupled cryo-EM. The size bar represents 20 nm. b Consultant 2D class averages of SA particle photos. The size bar represents 5 nm. c The 3D reconstruction of apo-SA at three.three Å decision from 23,991 particles and d the 3D reconstruction of the biotin-bound SA at three.2 Å decision from 45,686 particles. e The fourier shell correlation (FSC) curves of the 2 reconstructions utilizing the gold-standard standards

Single-particle reconstruction of SA by VPP-cryo-EM

Utilizing the automated particle choosing algorithm Gautomatch, we extracted ~710,000 and 1,350,000 particle photos from the great motion-corrected micrographs of SA within the absence and presence of biotin, respectively, and utilized a 120 Å Fourier high-pass filter to the particles previous to additional processing (Supplementary Fig. 2). The high-pass filter turned out to be needed for the proper alignment of the particle photos (Supplementary Fig. 2), most likely lowering the low-frequency background bias, in settlement with our earlier outcomes27. Reference-free two-dimensional (2D) alignment and classification from such datasets yielded 2D class averages with clear secondary structural options that matched the atomic mannequin of the SA protein (Supplementary Fig. 2B and 2C). Utilizing an preliminary mannequin generated de novo by the Stochastic Gradient Descent (SGD) technique in Relion6, we carried out a number of rounds of three-dimensional (3D) classifications to display screen one of the best particles for the ultimate 3D refinement and reconstruction (Supplementary Figs. three and four). Ultimately, we obtained a reconstruction of apo-SA at three.three Å decision (with D2 symmetry utilized through the refinement, Fig. 1c) from a ultimate dataset composed of ~24,000 particles (Supplementary Desk 1) and a reconstruction of the SA–biotin complicated at three.2 Å decision (with D2 symmetry utilized through the refinement, Fig. 1d) from a ultimate dataset comprising ~45,000 particles (Fig. 1e, Supplementary Desk 1). We additionally carried out reconstructions of the 2 completely different states with out imposing any symmetry (Supplementary Fig. 5A). These reconstructions have a really comparable map high quality to these calculated with the D2 symmetry, albeit with barely decrease resolutions (Supplementary Fig. 5C).

The 3D reconstructions of SA in its apo- and biotin-bound states had been each clear sufficient to depict all of the secondary structural parts and many of the aspect chains (Figs. 2 and three, Supplementary Film 1). The atomic mannequin of SA solved beforehand by X-ray crystallography (PDB 1MEP28) can match into the EM densities with a correlation coefficient ~zero.74, indicating the structural constancy of SA in its crystallographic and soluble varieties. The density of biotin within the SA–biotin reconstruction may be exactly recognized with the unambiguous docking of biotin’s atomic mannequin (Fig. 2). In contrast with the biotin-bound SA, the density equivalent to loop 46–51 within the EM map of apo-SA was lacking (Fig. 2), indicating that this lid-like loop is versatile with out ligand binding. In distinction, this loop may be clearly outlined within the EM map of biotin-bound SA, during which the most important aspect chains (ASN23, SER27, TYR43, ASN49, and SER88) forming a steady hydrogen bond community across the biotin ligand are nicely resolved (Fig. 2).

Fig. 2figure2

Comparability between the reconstructions of the 2 SA states. a, c The area across the biotin-binding pocket of the apo-SA EM map has an empty density of the pocket and a lacking loop 46–51 density, whereas in b, d the biotin-bound SA EM map, these two densities are nicely resolved with the atomic mannequin of the biotin ligand and the loop 46–51

Fig. threefigure3

Biotin-SA native maps with their corresponding atomic fashions. a Biotin density within the binding pocket. b Consultant densities of secondary buildings: β-sheet (b, c) and α-helix (d)

Targeted classification evaluation of the biotin-binding pocket

A essential downside in drug discovery is to establish the ligand-binding web site of goal proteins. We puzzled whether or not the ligand-binding web site may very well be decided by way of picture processing in small proteins reminiscent of SA with out prior information29,30,31,32,33. As SA is a tetramer and has 4 biotin-binding websites in every protein, we handled every SA monomer (with one binding pocket) as an uneven unit and used the angular info from the reconstruction with D2 symmetry to align the 4 uneven models from the identical particle to a given orientation. This step generated a dataset 4 instances bigger and comprising roughly aligned uneven particles, thus referred to as the uneven particle dataset. After an area search refinement with C1 symmetry, the uneven particle dataset was subjected to 35 iterations of 3D classification into four lessons in a skip-alignment mode in Relion. With out particularly specializing in the binding pocket, a tender masks barely bigger than the SA monomer was utilized in both the refinement or classification. We carried out this 3D skip-alignment classification evaluation of the apo-SA and biotin-SA datasets individually, and located a slightly small occupancy variance across the biotin-binding pocket among the many completely different lessons in every dataset (Supplementary Fig. 6A and 6B), demonstrating unambiguously the dearth of biotin in all of the monomers of apo-SA and the total occupancy of biotin in all of the monomers of biotin-SA. This consequence happens as a result of SA has a really sturdy binding affinity to biotin and the situation of the biotin-SA specimen allowed the total occupancy of the protein’s ligand-binding websites. The ligand occupancy, nevertheless, is probably not full for different proteins and different circumstances. Thus, we tried to check whether or not we might extract the ligand-binding info by picture processing from particles with a partial ligand occupancy. We blended the apo-SA and biotin-bound SA datasets, and analysed them as one dataset for the 3D refinement. The reconstruction of the blended dataset demonstrated a construction displaying a biotin-like density within the binding pocket at three.1 Å decision (Fig. 4a, b, Supplementary Fig. 5B). From this blended dataset of apo-SA and biotin-SA, the 3D skip-alignment classification of the uneven unit into 4 lessons illustrated distinct variations within the biotin-binding pocket (Fig. 4c). Though Class II was vacant of biotin, the opposite three lessons all had partial biotin occupancy within the binding pocket. We additional refined the 3D reconstructions utilizing particles in Class II (Fig. 4d) or the merged Class I–III–IV (Fig. 4e) individually. The refined 3D maps confirmed extra clearly that the Class II reconstruction lacked a density equivalent to loop 46–51 and the biotin ligand (Fig. 4d, pink circle), whereas the Class I–III–IV reconstruction maintained each clearly (Fig. 4e, blue circle).

Fig. fourfigure4

Reconstruction and classification utilizing the blended dataset. a The 3D reconstruction of the blended dataset (apo-SA + biotin-SA) with three.1 Å decision demonstrates a biotin-bound-like density (circled in blue) as b the 3D reconstruction of biotin-SA at three.2 Å decision of a monomer. c Uneven 3D classification reconstructions of the blended dataset. The empty density of the biotin-binding pocket within the monomer of the Class II reconstruction is circled in pink in distinction to the ligand densities within the different lessons. The share of particles and ligand occupancy in every class are labeled. A column graph with error bars to indicate the ligand occupancy of every class is proven. The 3D reconstruction of d class II and e the merged class I–III–IV indicated the apo-SA and biotin-SA individually. A aspect part comparability demonstrated the additional density of loop 46–51 and the biotin molecule in e (blue circle). Error bars (SD) had been calculated from three random repeats. Supply knowledge are supplied as a Supply Knowledge file

We additional randomly cut up the biotin-SA dataset into 20 subsets (9140 monomers in every subset) and blended completely different numbers of them with the apo-SA dataset to generate 20 blended datasets with completely different ratios of biotin-SA/apo-SA. We then carried out the 3D refinement of those blended datasets. Because the biotin-SA/apo-SA ratio elevated, the density of loop 46–51 and biotin molecules within the reconstructions grew to become clearer and was recognizable when the ratio was increased than zero.5 (Supplementary Fig. 6C). From the blended dataset of M5 with a biotin-SA/apo-SA ratio of zero.5, we might additional classify it to separate the biotin-bound SA structural options (Supplementary Fig. 6D). The outcomes above implicated the potential of the heterogeneity evaluation for the ligand-binding detection of proteins as small as SA by single-particle cryo-EM.

Reconstruction of sub-tetrameric SA from subtracted dataset

Though the 52 kDa SA is the smallest protein that has been resolved at near-atomic decision utilizing SPA cryo-EM till now, we had been questioning whether or not SPA cryo-EM is able to reconstructing even smaller proteins. We used the particle segmentation and subtraction algorithms34,35 which are at present accessible in Relion to generate monomeric (13 kDa), dimeric (26 kDa), and trimeric (39 kDa) SA datasets from uncooked biotin-SA datasets in silica (Fig. 5a). The subtracted SA datasets had smaller molecular weights and broke the intrinsic D2 symmetry of SA and due to this fact the sign for the correct alignment was even weaker.

Fig. 5figure5

Reconstructions of subtracted SA in several oligomeric states. a The diagrammatic sketch of the subtraction in uncooked biotin-SA particles. The white components had been subtracted from the person particle photos based mostly on associated angular info, with the blue half left for picture processing (monomer, dimer, and trimer from left to proper). b 2D classification outcomes from subtracted datasets in several oligomeric states both utilizing the angular info generated from the 3D refinement of the SA tetramers (Skip Align) or omitting the angular info in a reference-free mode (Search Align). The size bar represents 5 nm. c 3D reconstructions with native angular search of the three subtracted datasets. The preliminary tough angular info was generated from the 3D refinement of the SA tetramers. d 3D reconstructions with world angular search. The outcomes point out that solely the trimeric dataset might yield a profitable world refinement from scratch

We first examined whether or not there was sufficient sign within the subtracted dataset for 2D classification with the proper angular info. The angular info of every subtracted particle was calculated in accordance with its relative orientation within the authentic tetrameric SA particle in addition to the angular info of that tetrameric SA picture within the ultimate tetramer reconstruction. When utilizing the proper angular info with out alignment, all three subtracted datasets generated good 2D class averages with appropriate shapes and options (Fig. 5b, Skip Align). By eradicating all of the angular info, we carried out the reference-free 2D alignment and classification of the three datasets from scratch in Relion. On this process, the 13 kDa monomeric dataset generated 2D class averages with roughly appropriate outlines however a lot noisier options than the superbly aligned controls in several views (Fig. 5b, Search Align, left panel), suggesting extra alignment error within the reference-free alignment. The 26 kDa dimeric dataset generated one well-aligned view (Fig. 5b, Search Align, center panel), whereas the opposite views had been misaligned. The 39 kDa trimeric dataset generated appropriate shapes and options in a number of views (Fig. 5b, proper panel as representatives), indicating a profitable reference-free alignment.

To confirm whether or not the subtracted datasets can nonetheless generate legitimate 3D reconstructions, we used the proper angular info to carry out native 3D refinement. Certainly, given the proper angular info, all of the three subtracted datasets yielded appropriate reconstructions (Fig. 5c). We additional examined whether or not the photographs from these three datasets had sufficient alerts to seek for the proper angular info with none prior information. The 39 kDa trimeric dataset had sufficient alerts to generate an accurate 3D reconstruction by way of a worldwide angular search from scratch (Fig. 5c). In distinction, the monomeric and dimeric datasets didn’t reconstruct high-resolution buildings in world refinement (Fig. 5d), most likely as a result of lack of enough alerts to align.

The 3D refinement outcomes of the three datasets had been in line with the 2D classification, indicating that: (1) all datasets contained sufficient alerts for reconstruction at excessive decision if the angular info is appropriate and (2) the 39 kDa trimeric SA photos already contained sufficient alerts for picture processing from scratch to acquire a high-resolution construction. The outcomes additionally indicated that good 2D class averages with clear options would supply a excessive chance of profitable reconstruction. In our outcomes, the 26 kDa dimeric dataset might generate high-quality 2D class averages of sure orientations however not the entire views. The dearth of accuracy of the alignments within the different orientations most likely induced the failure of its 3D refinement. We infer that the most important constituents of the β-strands in SA made the alignment tough in some orientations. Nonetheless, the profitable reconstruction of the trimer dataset indicated the potential of fixing an uneven protein construction with a molecular weight ~39 kDa at near-atomic decision by SPA cryo-EM.

Distribution of SA particles within the vitrified specimen

We observed that even after the cautious scrutiny of the SA particle photos by 2D classification to take away all apparent junk or unhealthy particles, solely ~20% (79,289 vs. 378,987 for the apo-SA, Supplementary Fig. three) of the seemingly good particles contributed to the proper high-resolution reconstruction after the 3D classification. Certainly, regardless of our numerous efforts on picture processing procedures, the opposite 80% of the particle photos didn’t generate reconstructions with clear secondary structural particulars, regardless that they appeared very comparable in our eyes to the great particles for the high-resolution reconstructions. We confirmed that the unique micrographs containing these particles had been of top quality.

We got down to examine what made the distinction for the particles to contribute to the high-resolution reconstruction. It has been hypothesized that the adsorption of protein molecules on the AWI could trigger the denaturation or partial unfolding of the protein3,10,11. We had been questioning whether or not the placement of the particles within the skinny layer of vitreous ice induced the variation of the picture high quality for the high-resolution reconstruction. We due to this fact carried out the electron tomography of the identical grid for the single-particle knowledge assortment of SA on the graphene-supporting movie utilizing VPP-Cs-corrector-coupled cryo-EM. The 3D reconstructions of the tomograms had been clear sufficient for us to depict the SA particle distribution within the specimen (Supplementary Motion pictures 2 and three, Fig. 6, and Supplementary Fig. 7). It’s attention-grabbing to see that the SA particles distributed primarily in two completely different layers alongside the z-direction, one on the AWI and the opposite on the graphene–water interface (GWI) (Fig. 6a, Supplementary Fig. 7). There have been only a few particles between these two layers. This statement means that through the specimen preparation, the SA molecules both caught to the GWI or bought adsorbed onto the AWI. Surprisingly, the particles on the GWI had an uneven distribution, principally in clustering areas (Fig. 6a, pink arrow) and just a few in lacuna areas (Fig. 6a, blue arrow). In distinction, the particles on AWI confirmed a extra uniform and dispersed distribution (Fig. 6b). Such a phenomenon was noticed in each comparatively thick (~50 nm, Supplementary Fig. 7C, Supplementary Film 2) and skinny (~10 nm, Supplementary Fig. 7D, Supplementary Film three) ice. The electron tomography evaluation implied that the micrographs of SA single particles collected at a zero-degree tilt truly mirrored the superposition of the particles on each GWI and AWI.

Fig. 6figure6

SA particles on graphene–water and air–water interfaces. a The X–Y cross-section equivalent to the graphene–water interface (GWI) from a reconstructed tomogram. The uneven distribution of particles is indicated as a clustering space (pink arrow) and lacuna space (blue arrow). The size bar represents 100 nm. b The X–Y cross-section equivalent to the air–water interface (AWI) from the identical reconstructed tomogram as in a. c A micrograph containing a clustering space (pink arrow) and uniform distribution space (blue arrow). The boundaries of the 2 areas are marked by dashed traces. The size bar represents 20 nm. d The identical micrograph as in c, with the particles that contributed to the ultimate high-resolution reconstruction circled in inexperienced. e The numbers of particles in Subset A and Subset B after the 2D Classification (After2D), after the primary 3D Classification (After3D), and within the ultimate Refinement (Remaining Refine) had been counted in 749 chosen micrographs with a transparent clustering characteristic. f The chances of particles from Subset A and Subset B within the completely different knowledge processing steps. g The distribution of the most important particle orientations, prime view (rounded-like) and aspect view (butterfly-like), in Subset A and Subset B, respectively. The particles in Subset B demonstrated a extreme preferential orientation. Supply knowledge are supplied as a Supply Knowledge file

We analysed all of the micrographs that had been used for the single-particle reconstruction by sorting them by the share of fine particles labeled within the appropriate high-resolution reconstruction. We discovered that one of the best micrographs with the very best percentages of fine particle photos had uneven particle distributions (Fig. 6c), and that the great particles contributing to the proper high-resolution reconstruction got here principally from the clustering areas with an analogous sample to these on the GWI, as revealed by electron tomography (Fig. 6d). The particles within the extra uniform and dispersed areas contributed a lot much less to the ultimate high-resolution reconstruction.

Intrigued by the statement of the particle distribution, we went by way of the complete apo-SA dataset to confirm the potential correlation between the particle distribution on the grids and their contribution to the high-resolution reconstructions. Out of the 1450 micrographs of apo-SA, we manually chosen 749 micrographs with clear options of particle clustering and extracted 212,105 particles from these micrographs utilizing the particle place info calculated from the earlier reference-free 2D alignment and classification of the complete apo-SA dataset. Based mostly on the placement of every particle, the 212,105 particles had been manually divided into two subsets with 134,606 particles within the clustering areas (subset A) and 77,499 particles within the uniformly dispersed areas (subset B) (Fig. 6a–d). Ideally, such a division ought to put many of the particles on the GWI in subset A and go away subset B with primarily particles on the AWI. We subsequently correlated the particles within the two subsets to the particles within the completely different steps through the 3D classification and refinement of the complete apo-SA dataset (Supplementary Fig. three). This assigned 44,326 particles from the 749 micrographs that contributed to the three.5 Å decision reconstruction after the primary spherical of 3D classification. We instantly observed that among the many 44,326 particles, 35,676, accounting for >80%, had been from subset A and solely eight,650, accounting for <20%, had been from subset B (Fig. 6e, f, Supplementary Desk 2). It's also value noting that the share of particles retained in one of the best 3D class from subset A is 26.5% (35,676/134,606; Supplementary Desk 2), increased than that from subset B, 11.1% (eight,650/77,499; Supplementary Desk 2). The truth that the contribution of the particles from subset A to one of the best 3D class elevated from 63.5% (134,606/212,105) to 80.5% (35,676/44,326) after the classification signifies bigger portion of the molecules on the GWI had been well-preserved.

To additional perceive the distinction between the 2 subsets of particles, we carried out a reference-free 2D classification on them and located that the subset B particles exhibited extra extreme preferential orientations than these of subset A (Fig. 6g, Supplementary Fig. 8A, B). We additionally in contrast the 3D reconstructions of the particles in subsets A and B, both utilizing angular info from the earlier 3D refinement of the complete apo-SA dataset or by recalculating them from scratch. The maps from subset A constantly demonstrated the proper options of the SA molecule, whereas the maps from subset B had been of poor high quality (Supplementary Figs. 8C, D, 9).

To additional examine the impact of AWI on the construction of SA molecules, we carried out cryo-EM evaluation of apo-SA on common holey carbon grids with out graphene assist. SPA of those SA molecules demonstrated a powerful preferential orientation, which has similarities to that of subset B within the above evaluation (Supplementary Fig. 10).

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