7V84

Local refinement of SARS-CoV-2 S-Gamma variant (P.1) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain

• PDB DOI: https://doi.org/10.2210/pdb7V84/pdb
• EM Map EMD-31789: EMDB EMDataResource

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


• Deposited: 2021-08-22 Released: 2021-10-06 
• Deposition Author(s): Yang, T.J., Yu, P.Y., Chang, Y.C., Hsu, S.T.D.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan), Academia Sinica (Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Local refinement of SARS-CoV-2 S-Gamma variant (P.1) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain

Yang, T.J., Yu, P.Y., Chang, Y.C., Hsu, S.T.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 243.31 kDa 
• Atom Count: 6,636 
• Modelled Residue Count: 797 
• Deposited Residue Count: 2,144 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,283	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2,Green fluorescent protein	B [auth F]	861	Homo sapiens	Mutation(s): 0  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 A0A059PIQ0 (Aequorea victoria) Explore A0A059PIQ0  Go to UniProtKB:  A0A059PIQ0
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
UniProt Groups	A0A059PIQ0Q9BYF1
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: Q9BYF1-1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D [auth C], E [auth D], F [auth E], G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Yang, T.J., Yu, P.Y., Chang, Y.C., Hsu, S.T.D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	109-3114-Y-001-001
Academia Sinica (Taiwan)	Taiwan	AS-CDA-109-L08
Academia Sinica (Taiwan)	Taiwan	AS-CFII-108-110
Academia Sinica (Taiwan)	Taiwan	AS-CFII108-111

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary