6YLA

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab

• PDB DOI:  https://doi.org/10.2210/pdb6YLA/pdb

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


• Deposited: 2020-04-06 Released: 2020-04-15 
• Deposition Author(s): Huo, J., Zhao, Y., Ren, J., Zhou, D., Ginn, H.M., Fry, E.E., Owens, R., Stuart, D.I.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.237 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

Literature

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.

Huo, J., Zhao, Y., Ren, J., Zhou, D., Duyvesteyn, H.M.E., Ginn, H.M., Carrique, L., Malinauskas, T., Ruza, R.R., Shah, P.N.M., Tan, T.K., Rijal, P., Coombes, N., Bewley, K.R., Tree, J.A., Radecke, J., Paterson, N.G., Supasa, P., Mongkolsapaya, J., Screaton, G.R., Carroll, M., Townsend, A., Fry, E.E., Owens, R.J., Stuart, D.I.

(2020) Cell Host Microbe 28: 445-454.e6

• PubMed: 32585135 
• DOI: https://doi.org/10.1016/j.chom.2020.06.010
• Primary Citation of Related Structures:  
  6YLA, 6YM0, 6YOR, 6Z97


• PubMed Abstract: 
  

There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment.

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Organizational Affiliation: 

Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, OX3 7BN, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK. 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.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 149.08 kDa 
• Atom Count: 10,090 
• Modelled Residue Count: 1,273 
• Deposited Residue Count: 1,324 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth E], D [auth A]	213	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	B [auth H], E [auth B]	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain	C [auth L], F [auth C]	220	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	GA [auth C], V [auth L]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
NAG	L [auth E], M [auth E], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG0	X [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
MLI	BA [auth B], CA [auth B], DA [auth B], EA [auth B], I [auth E], JA [auth C], KA [auth C], LA [auth C], N [auth E], O [auth H], R [auth H], S [auth H]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
DMS	AA [auth A], FA [auth B], G [auth E], H [auth E], HA [auth C], IA [auth C], J [auth E], K [auth E], P [auth H], Q [auth H], T [auth L], U [auth L], W [auth A], Y [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.237 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.124	α = 90
b = 163.124	β = 90
c = 189.076	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Huo, J., Zhao, Y., Ren, J., Zhou, D., Ginn, H.M., Fry, E.E., Owens, R., Stuart, D.I.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2020-10-28
  Changes: Database references, Structure summary