7V88

Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form

PDB DOI: https://doi.org/10.2210/pdb7V88/pdb
EM Map EMD-31793: EMDB EMDataResource

Classification: VIRAL PROTEIN
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: 3.30 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-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form

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

To be published.

Macromolecule Content

Total Structure Weight: 641.71 kDa
Atom Count: 35,098
Modelled Residue Count: 4,281
Deposited Residue Count: 5,565
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	1,281	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 13 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: 16	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence AnnotationsExpand
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,Angiotensin-converting enzyme 2 (ACE2) ectodomain	D [auth F], E [auth G]	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: 2	Glycosylation Focus chain D [auth F] Focus chain E [auth G]	Go to GlyGen: Q9BYF1-1
Sequence AnnotationsExpand
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], F [auth D], FA [auth f], G [auth E], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth 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 F [auth D] Focus chain FA [auth f] Focus chain G [auth E] 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 KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth 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 F [auth D] Focus chain FA [auth f] Focus chain G [auth E] 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 KA [auth k] Focus chain L Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth 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 AB [auth C] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain DB [auth G] SDF format, chain EB [auth G] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain CB [auth F] mmCIF format, chain DB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AB [auth C] BB [auth F] CB [auth F] DB [auth G] EB [auth G] AB [auth C], BB [auth F], CB [auth F], DB [auth G], EB [auth G], QA [auth A], RA [auth A], SA [auth A], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth C], 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 F] Focus chain CB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] 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 C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] 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 C] Focus chain ZA [auth C]

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
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