7V83

Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2

PDB DOI: https://doi.org/10.2210/pdb7V83/pdb
EM Map EMD-31788: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2

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

To be published.

Macromolecule Content

Total Structure Weight: 740.72 kDa
Atom Count: 40,162
Modelled Residue Count: 4,902
Deposited Residue Count: 6,432
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2,Green fluorescent protein	D, E, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A0A059PIQ0Q9BYF1
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain D	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

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	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain G Focus chain GA [auth g] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain IA [auth i] Focus chain J Focus chain JA [auth j] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain EB [auth C] SDF format, chain FB [auth C] SDF format, chain IB [auth D] SDF format, chain KA [auth A] SDF format, chain LB [auth D] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain XA [auth B] SDF format, chain ZA [auth C] SDF format, chain AB [auth C] SDF format, chain DB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth D] SDF format, chain JB [auth D] SDF format, chain KB [auth D] SDF format, chain LA [auth A] SDF format, chain MB [auth D] SDF format, chain SA [auth B] SDF format, chain WA [auth B] SDF format, chain YA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain IB [auth D] MOL2 format, chain KA [auth A] MOL2 format, chain LB [auth D] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain SA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain IB [auth D] mmCIF format, chain KA [auth A] mmCIF format, chain LB [auth D] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth D] mmCIF format, chain JB [auth D] mmCIF format, chain KB [auth D] mmCIF format, chain LA [auth A] mmCIF format, chain MB [auth D] mmCIF format, chain SA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain YA [auth B]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth D], IB [auth D], JB [auth D], KA [auth A], KB [auth D], LA [auth A], LB [auth D], MA [auth A], MB [auth D], NA [auth A], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth A] Focus chain MB [auth D] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KA [auth A] Focus chain KB [auth D] Focus chain LA [auth A] Focus chain LB [auth D] Focus chain MA [auth A] Focus chain MB [auth D] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

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