7WNM

Structure of SARS-CoV-2 Gamma variant receptor-binding domain complexed with high affinity human ACE2 mutant (T27F,R273Q)

• PDB DOI: https://doi.org/10.2210/pdb7WNM/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-01-18 Released: 2022-12-21 
• Deposition Author(s): Ma, R.Y., Han, P.C., Wang, Q.H., Han, P.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

A binding-enhanced but enzymatic activity-eliminated human ACE2 efficiently neutralizes SARS-CoV-2 variants.

Zheng, A., Wu, L., Ma, R., Han, P., Huang, B., Qiao, C., Wang, Q., Tan, W., Gao, G.F., Han, P.

(2022) Signal Transduct Target Ther 7: 10-10

• PubMed: 35013100 
• DOI: https://doi.org/10.1038/s41392-021-00821-y
• Primary Citation of Related Structures:  
  7WNM

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 113.35 kDa 
• Atom Count: 6,521 
• Modelled Residue Count: 790 
• Deposited Residue Count: 984 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A [auth B]	740	Homo sapiens	Mutation(s): 2  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth A]	244	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 3  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.346	α = 90
b = 103.346	β = 90
c = 233.324	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: 2022-12-21 
Deposition Author(s): Ma, R.Y., Han, P.C., Wang, Q.H., Han, P.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFC0863300

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary