7WHH | pdb_00007whh

Crystal structure of SARS-CoV-2 omicron RBD and human ACE2

• PDB DOI: https://doi.org/10.2210/pdb7WHH/pdb

• Classification: HYDROLASE/VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2021-12-30 Released: 2022-06-01 
• Deposition Author(s): Wang, X.Q., Lan, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.231 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction.

Lan, J., He, X., Ren, Y., Wang, Z., Zhou, H., Fan, S., Zhu, C., Liu, D., Shao, B., Liu, T.Y., Wang, Q., Zhang, L., Ge, J., Wang, T., Wang, X.

(2022) Cell Res 32: 593-595

• PubMed: 35418218 
• DOI: https://doi.org/10.1038/s41422-022-00644-8
• Primary Citation Related Structures: 
  7WHH

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Organizational Affiliation: 
• The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China.
Microsoft Research Asia, Beijing, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China.
Department of Chemistry, Tsinghua University, Beijing, China.
Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, and Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China. [e-mail].
The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Microsoft Research Asia, Beijing, China. [e-mail].
The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China. [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: 92.85 kDa 
• Atom Count: 6,667 
• Modeled Residue Count: 792 
• Deposited Residue Count: 792 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	598	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth E]	194	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15  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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.231 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.706	α = 90
b = 104.706	β = 90
c = 227.098	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Wang, X.Q., Lan, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary
• Version 1.3: 2025-06-18
  Changes: Database references