7DWY

S protein of SARS-CoV-2 in the locked conformation

PDB DOI: https://doi.org/10.2210/pdb7DWY/pdb
EM Map EMD-30889: EMDB EMDataResource

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

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: 2.70 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: 446.07 kDa
Atom Count: 26,979
Modelled Residue Count: 3,297
Deposited Residue Count: 3,849
Unique protein chains: 1

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 Membrane Entity: Yes
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: 18	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H D, E, F, G, H, I, J, K, L, M, N	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EIC Query on EIC Download Ideal Coordinates CCD File SDF format, chain DB [auth B] SDF format, chain HA [auth A] SDF format, chain XB [auth C] MOL2 format, chain DB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain XB [auth C] mmCIF format, chain DB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain XB [auth C]	DB [auth B], HA [auth A], XB [auth C]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain DB [auth B] Focus chain HA [auth A] Focus chain XB [auth C] Interactions & Density Focus chain DB [auth B] Focus chain HA [auth A] Focus chain XB [auth C]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain FA [auth A] SDF format, chain FB [auth C] SDF format, chain GA [auth A] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain IA [auth B] SDF format, chain IB [auth C] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain IB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain TB [auth C] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth C], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], P [auth A], PA [auth B], PB [auth C], Q [auth A], QA [auth B], QB [auth C], R [auth A], RA [auth B], RB [auth C], S [auth A], SA [auth B], SB [auth C], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], V [auth A], VA [auth B], VB [auth C], W [auth A], WA [auth B], WB [auth C], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HB [auth C] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 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

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2021-06-16
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary