7DK2 | pdb_00007dk2

Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab

• PDB DOI: https://doi.org/10.2210/pdb7DK2/pdb

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


• Deposited: 2020-11-22 Released: 2021-12-08 
• Deposition Author(s): Wang, J., Jiao, S., Wang, R., Zhang, J., Zhang, M., Wang, M., Chen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Models: experimental

Literature

Architectural versatility of spike neutralization by a SARS-CoV-2 antibody

Sun, Y., Liu, F.J., Guo, H.T., Wang, J., Wang, R., Zhang, M., Wang, M., Chen, S.

To be published.

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 generated by PISA (software)

Biological Assembly Evidence: gel filtration

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 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 290.03 kDa 
• Atom Count: 19,459 
• Modeled Residue Count: 2,503 
• Deposited Residue Count: 2,640 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MW07 heavy chain	A, D, G, J	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MW07 light chain	B, E, H, K	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C, F, I, L	223	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	M [auth C], N [auth F], O [auth I], P [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.304 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.73	α = 90
b = 102.81	β = 107.16
c = 163.42	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Wang, J., Jiao, S., Wang, R., Zhang, J., Zhang, M., Wang, M., Chen, S.

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary