8FAH | pdb_00008fah

Crystal structure of SARS-CoV-2 receptor binding domain in complex with SARS-CoV-2 reactive human antibody CR3022

• PDB DOI: https://doi.org/10.2210/pdb8FAH/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-11-26 Released: 2023-12-13 
• Deposition Author(s): Sankhala, R.S., Jensen, J.L., Joyce, M.G.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.22 Å
• R-Value Free: 
  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Models: experimental

Literature

Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.

Sankhala, R.S., Dussupt, V., Chen, W.H., Bai, H., Martinez, E.J., Jensen, J.L., Rees, P.A., Hajduczki, A., Chang, W.C., Choe, M., Yan, L., Sterling, S.L., Swafford, I., Kuklis, C., Soman, S., King, J., Corbitt, C., Zemil, M., Peterson, C.E., Mendez-Rivera, L., Townsley, S.M., Donofrio, G.C., Lal, K.G., Tran, U., Green, E.C., Smith, C., de Val, N., Laing, E.D., Broder, C.C., Currier, J.R., Gromowski, G.D., Wieczorek, L., Rolland, M., Paquin-Proulx, D., van Dyk, D., Britton, Z., Rajan, S., Loo, Y.M., McTamney, P.M., Esser, M.T., Polonis, V.R., Michael, N.L., Krebs, S.J., Modjarrad, K., Joyce, M.G.

(2024) Structure 32: 131

• PubMed: 38157856 
• DOI: https://doi.org/10.1016/j.str.2023.11.015
• Primary Citation Related Structures: 
  7U8E, 8FAH, 8SGU, 8SMI, 8SMT


• PubMed Abstract: 
  

  Given the continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs), immunotherapeutics that target conserved epitopes on the spike (S) glycoprotein have therapeutic advantages. Here, we report the crystal structure of the SARS-CoV-2 S receptor-binding domain (RBD) at 1.95 Å and describe flexibility and distinct conformations of the angiotensin-converting enzyme 2 (ACE2)-binding site. We identify a set of SARS-CoV-2-reactive monoclonal antibodies (mAbs) with broad RBD cross-reactivity including SARS-CoV-2 Omicron subvariants, SARS-CoV-1, and other sarbecoviruses and determine the crystal structures of mAb-RBD complexes with Ab246 and CR3022 mAbs targeting the class IV site, WRAIR-2134, which binds the recently designated class V epitope, and WRAIR-2123, the class I ACE2-binding site. The broad reactivity of class IV and V mAbs to conserved regions of SARS-CoV-2 VoCs and other sarbecovirus provides a framework for long-term immunotherapeutic development strategies.

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Organizational Affiliation: 
• Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA.
U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA.
Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. Electronic address: [e-mail].
Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.45 kDa 
• Atom Count: 4,969 
• Modeled Residue Count: 641 
• Deposited Residue Count: 649 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CR3022 Fab heavy chain	A [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR3022 Fab light chain	B [auth L]	220	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth A]	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.22 Å
• R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.176	α = 90
b = 151.176	β = 90
c = 192.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Sankhala, R.S., Jensen, J.L., Joyce, M.G.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	W81XWH-18-2-0040

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Database references
• Version 1.2: 2024-02-14
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Structure summary