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Yorodumi- PDB-7n64: SARS-CoV-2 Spike (2P) in complex with G32R7 Fab (RBD and NTD loca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n64 | ||||||
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Title | SARS-CoV-2 Spike (2P) in complex with G32R7 Fab (RBD and NTD local reconstruction) | ||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / coronavirus / antibody / epitope / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | ||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Windsor, I.W. / Jenni, S. / Tong, P. / Gautam, A.K. / Wesemann, D.R. / Harrison, S.C. | ||||||
Citation | Journal: bioRxiv / Year: 2021 Title: Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike. Authors: Pei Tong / Avneesh Gautam / Ian Windsor / Meghan Travers / Yuezhou Chen / Nicholas Garcia / Noah B Whiteman / Lindsay G A McKay / Felipe J N Lelis / Shaghayegh Habibi / Yongfei Cai / Linda J ...Authors: Pei Tong / Avneesh Gautam / Ian Windsor / Meghan Travers / Yuezhou Chen / Nicholas Garcia / Noah B Whiteman / Lindsay G A McKay / Felipe J N Lelis / Shaghayegh Habibi / Yongfei Cai / Linda J Rennick / W Paul Duprex / Kevin R McCarthy / Christy L Lavine / Teng Zuo / Junrui Lin / Adam Zuiani / Jared Feldman / Elizabeth A MacDonald / Blake M Hauser / Anthony Griffths / Michael S Seaman / Aaron G Schmidt / Bing Chen / Donna Neuberg / Goran Bajic / Stephen C Harrison / Duane R Wesemann / Abstract: Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted ...Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants. #1: Journal: Cell(Cambridge,Mass.) / Year: 2021 Title: Memory B Cell Repertoire for Recognition of Evolving SARS-CoV-2 Spike Authors: Tong, P. / Gautam, A.K. / Windsor, I.W. / Bajic, G. / Harrison, S.C. / Wesemann, D.R. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7n64.cif.gz | 207.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n64.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 7n64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n64_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7n64_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7n64_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 7n64_validation.cif.gz | 54.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/7n64 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/7n64 | HTTPS FTP |
-Related structure data
Related structure data | 24193MC 7n62C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 141297.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): expi293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25235.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293F / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23369.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293F / Production host: Homo sapiens (human) |
-Sugars , 3 types, 4 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SARS-CoV-2 Spike in complex with G32R7 Fab / Type: COMPLEX Details: B cell receptor was sequenced from memory B cell of SARS-CoV-2 convalescent human patient and express as Fab. SARS-CoV2-2 surface protein (with 2P stabilizing mutations) was expressed as soluble ectodomain. Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Strain: expi293F / Cell: human embryonic kidney / Plasmid: pVRC | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 88 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: -2500 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.8 sec. / Electron dose: 56.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1373975 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176303 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.44 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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