9IUP | pdb_00009iup

KP.3 RBD in complex with ACE2

• PDB DOI: https://doi.org/10.2210/pdb9IUP/pdb
• EM Map EMD-60911: EMDB EMDataResource

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


• Deposited: 2024-07-22 Released: 2025-01-15 
• Deposition Author(s): Feng, L.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2.

Feng, L., Sun, Z., Zhang, Y., Jian, F., Yang, S., Xia, K., Yu, L., Wang, J., Shao, F., Wang, X., Cao, Y.

(2024) Cell Discov 10: 123-123

• PubMed: 39616168 
• DOI: https://doi.org/10.1038/s41421-024-00752-2
• Primary Citation of Related Structures:  
  9IUP, 9IUQ, 9IUU

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Organizational Affiliation: 
• CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Changping Laboratory, Beijing, China.
Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China.
School of Biological Sciences, University of Cambridge, Cambridge, UK.
CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Changping Laboratory, Beijing, China. [e-mail].
Biomedical Pioneering Innovation Center (BIOPIC), Peking 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 (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 91.15 kDa 
• Atom Count: 6,420 
• Modeled Residue Count: 787 
• Deposited Residue Count: 787 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	594	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	193	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 8  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth B], D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Feng, L.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection