+Open data
-Basic information
Entry | Database: PDB / ID: 8vcr | ||||||
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Title | SARS-CoV-2 Spike S2 bound to Fab 54043-5 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 spike / S2 subunit / viral fusion / monoclonal antibody | ||||||
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 / receptor-mediated endocytosis of virus by host cell / membrane fusion / 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: 3 Å | ||||||
Authors | Johnson, N.V. / McLellan, J.S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody Authors: Johnson, N.V. / Wall, S.C. / Kramer, K.J. / Holt, C.M. / Periasamy, S. / Richardson, S. / Suryadevara, N. / Andreano, E. / Paciello, I. / Pierleoni, G. / Piccini, G. / Huang, Y. / Ge, P. / ...Authors: Johnson, N.V. / Wall, S.C. / Kramer, K.J. / Holt, C.M. / Periasamy, S. / Richardson, S. / Suryadevara, N. / Andreano, E. / Paciello, I. / Pierleoni, G. / Piccini, G. / Huang, Y. / Ge, P. / Allen, J.D. / Uno, N. / Shiakolas, A.R. / Pilewski, K.A. / Nargi, R.S. / Sutton, R.E. / Abu-Shmais, A.A. / Parks, R. / Haynes, B.F. / Carnahan, R.H. / Crowe Jr., J.E. / Rappuoli, R. / Bukreyev, A. / Ross, T.M. / Sautto, G.A. / McLellan, J.S. / Georgiev, I.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vcr.cif.gz | 378 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vcr.ent.gz | 297.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vcr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8vcr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8vcr_validation.xml.gz | 71.5 KB | Display | |
Data in CIF | 8vcr_validation.cif.gz | 105.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/8vcr ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vcr | HTTPS FTP |
-Related structure data
Related structure data | 43139MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 65948.469 Da / Num. of mol.: 3 Mutation: S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): Freestyle 293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 25130.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) #3: Antibody | Mass: 23294.916 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / 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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.18.2_3874: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126621 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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