7DX9

Trypsin-digested S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 3 (3 up RBD and 2 PD bound)

PDB DOI: https://doi.org/10.2210/pdb7DX9/pdb
EM Map EMD-30900: EMDB EMDataResource

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

Deposited: 2021-01-18 Released: 2021-03-31
Deposition Author(s): Yan, R.H., Zhang, Y.Y., Li, Y.N., Ye, F.F., Guo, Y.Y., Xia, L., Zhong, X.Y., Chi, X.M., Zhou, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2.

Yan, R., Zhang, Y., Li, Y., Ye, F., Guo, Y., Xia, L., Zhong, X., Chi, X., Zhou, Q.

(2021) Cell Res 31: 717-719

PubMed: 33737693 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-021-00490-0
Primary Citation of Related Structures:
7DWX, 7DWY, 7DWZ, 7DX0, 7DX1, 7DX2, 7DX3, 7DX5, 7DX6, 7DX7, 7DX8, 7DX9

Organizational Affiliation

Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China. yanrenhong@westlake.edu.cn.

Macromolecule Content

Total Structure Weight: 635.45 kDa
Atom Count: 34,620
Modelled Residue Count: 4,209
Deposited Residue Count: 5,483
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(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): 2 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Go to UniProtKB: P0DTC2
Glycosylation
Glycosylation Sites: 16	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	D, E	817	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 Q9BYF1 (Homo sapiens) Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain D Focus chain E	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], F, FA [auth f], G, GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, KA [auth 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 F 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 KA [auth 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 F 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 KA [auth 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 (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain EB [auth C] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain UA [auth A] SDF format, chain YA [auth B] SDF format, chain AB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth C] SDF format, chain FB [auth C] SDF format, chain IB [auth C] SDF format, chain JB [auth C] SDF format, chain KB [auth C] SDF format, chain LB [auth C] SDF format, chain MB [auth D] SDF format, chain NA [auth A] SDF format, chain NB [auth E] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain FB [auth C] MOL2 format, chain IB [auth C] MOL2 format, chain JB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain LB [auth C] MOL2 format, chain MB [auth D] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain AB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain FB [auth C] mmCIF format, chain IB [auth C] mmCIF format, chain JB [auth C] mmCIF format, chain KB [auth C] mmCIF format, chain LB [auth C] mmCIF format, chain MB [auth D] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth E] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain ZA [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth C] EB [auth C] AB [auth B], BB [auth B], CB [auth B], DB [auth C], EB [auth C], FB [auth C], GB [auth C], HB [auth C], IB [auth C], JB [auth C], KB [auth C], LA [auth A], LB [auth C], MA [auth A], MB [auth D], NA [auth A], NB [auth E], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth D] Focus chain NA [auth A] Focus chain NB [auth E] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IB [auth C] Focus chain JB [auth C] Focus chain KB [auth C] Focus chain LA [auth A] Focus chain LB [auth C] Focus chain MA [auth A] Focus chain MB [auth D] Focus chain NA [auth A] Focus chain NB [auth E] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.6

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971123
National Natural Science Foundation of China (NSFC)	China	81920108015
National Natural Science Foundation of China (NSFC)	China	31930059