6XCA | pdb_00006xca

Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C105

• PDB DOI: https://doi.org/10.2210/pdb6XCA/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-08 Released: 2020-07-01 
• Deposition Author(s): Sharaf, N.G., Barnes, C.O., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies.

Barnes, C.O., West Jr., A.P., Huey-Tubman, K.E., Hoffmann, M.A.G., Sharaf, N.G., Hoffman, P.R., Koranda, N., Gristick, H.B., Gaebler, C., Muecksch, F., Lorenzi, J.C.C., Finkin, S., Hagglof, T., Hurley, A., Millard, K.G., Weisblum, Y., Schmidt, F., Hatziioannou, T., Bieniasz, P.D., Caskey, M., Robbiani, D.F., Nussenzweig, M.C., Bjorkman, P.J.

(2020) Cell 182: 828

• PubMed: 32645326 
• DOI: https://doi.org/10.1016/j.cell.2020.06.025
• Primary Citation Related Structures: 
  6XCA, 6XCM, 6XCN


• PubMed Abstract: 
  

  Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1 ^A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.

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Organizational Affiliation: 
• Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
Hospital Program Direction, The Rockefeller University, New York, NY, USA.
Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA. Electronic address: [e-mail].
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.71 kDa 
• Atom Count: 3,632 
• Modeled Residue Count: 422 
• Deposited Residue Count: 447 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C105 Heavy Chain	A [auth H]	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C105 Light Chain	B [auth L]	217	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth H], D [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.413	α = 90
b = 120.081	β = 90
c = 123.329	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Sharaf, N.G., Barnes, C.O., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01-AI138398-S1

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-07-22
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary