7YDI

SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD region

• PDB DOI: https://doi.org/10.2210/pdb7YDI/pdb
• EM Map EMD-33748: EMDB EMDataResource

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


• Deposited: 2022-07-04 Released: 2022-08-24 
• Deposition Author(s): Liu, B., Gao, X., Li, Z., Chen, X., He, J., Chen, L., Xiong, X.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7YEG

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 138.57 kDa 
• Atom Count: 9,675 
• Modelled Residue Count: 1,229 
• Deposited Residue Count: 1,237 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	602	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885
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 E]	193	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of R1-32	C [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of R1-32	D [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Liu, B., Gao, X., Li, Z., Chen, X., He, J., Chen, L., Xiong, X.

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Funding Organization	Location	Grant Number
Other government	China	82041014

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-05-03
  Changes: Database references
• Version 1.2: 2023-07-26
  Changes: Other