7CT5 | pdb_00007ct5

S protein of SARS-CoV-2 in complex bound with T-ACE2

PDB DOI: https://doi.org/10.2210/pdb7CT5/pdb
EM Map EMD-30460: EMDB EMDataResource

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

Deposited: 2020-08-18 Released: 2020-11-18
Deposition Author(s): Guo, L., Bi, W.W., Zhang, Y.Y., Yan, R.H., Li, Y.N., Zhou, Q., Dang, B.B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Engineered trimeric ACE2 binds viral spike protein and locks it in "Three-up" conformation to potently inhibit SARS-CoV-2 infection.

Guo, L., Bi, W., Wang, X., Xu, W., Yan, R., Zhang, Y., Zhao, K., Li, Y., Zhang, M., Cai, X., Jiang, S., Xie, Y., Zhou, Q., Lu, L., Dang, B.

(2021) Cell Res 31: 98-100

PubMed: 33177651 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-020-00438-w
Primary Citation Related Structures:
7CT5

Organizational Affiliation

Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.

Macromolecule Content

Total Structure Weight: 674.91 kDa
Atom Count: 39,626
Modeled Residue Count: 4,804
Deposited Residue Count: 5,814
Unique protein chains: 2

Macromolecules

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| 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) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	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:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	D, E, F	655	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain D Focus chain E Focus chain F	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth 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 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 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 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 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 B] SDF format, chain CB [auth B] SDF format, chain DB [auth B] SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain IB [auth B] SDF format, chain JB [auth B] SDF format, chain LB [auth C] SDF format, chain MB [auth C] SDF format, chain OB [auth C] SDF format, chain PA [auth A] SDF format, chain PB [auth C] SDF format, chain QB [auth C] SDF format, chain RB [auth C] SDF format, chain SA [auth A] SDF format, chain SB [auth C] SDF format, chain TA [auth A] SDF format, chain TB [auth C] SDF format, chain UA [auth A] SDF format, chain VB [auth E] SDF format, chain WA [auth A] SDF format, chain WB [auth F] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] SDF format, chain XA [auth A] SDF format, chain VA [auth A] SDF format, chain UB [auth D] SDF format, chain RA [auth A] SDF format, chain QA [auth A] SDF format, chain NB [auth C] SDF format, chain KB [auth C] SDF format, chain HB [auth B] SDF format, chain EB [auth B] SDF format, chain AB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain MB [auth C] MOL2 format, chain OB [auth C] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain SA [auth A] MOL2 format, chain SB [auth C] MOL2 format, chain TA [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain UA [auth A] MOL2 format, chain VB [auth E] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth F] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain XA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain UB [auth D] MOL2 format, chain RA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain KB [auth C] MOL2 format, chain HB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain AB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain MB [auth C] mmCIF format, chain OB [auth C] mmCIF format, chain PA [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain RB [auth C] mmCIF format, chain SA [auth A] mmCIF format, chain SB [auth C] mmCIF format, chain TA [auth A] mmCIF format, chain TB [auth C] mmCIF format, chain UA [auth A] mmCIF format, chain VB [auth E] mmCIF format, chain WA [auth A] mmCIF format, chain WB [auth F] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain XA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain UB [auth D] mmCIF format, chain RA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain KB [auth C] mmCIF format, chain HB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain AB [auth B]	AB [auth B] BB [auth B] CB [auth B] DB [auth B] EB [auth B] AB [auth B], BB [auth B], CB [auth B], DB [auth B], EB [auth B], FB [auth B], GB [auth B], HB [auth B], IB [auth B], JB [auth B], KB [auth C], LB [auth C], MB [auth C], NB [auth C], OB [auth C], PA [auth A], PB [auth C], QA [auth A], QB [auth C], RA [auth A], RB [auth C], SA [auth A], SB [auth C], TA [auth A], TB [auth C], UA [auth A], UB [auth D], VA [auth A], VB [auth E], WA [auth A], WB [auth F], XA [auth A], 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 B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain UA [auth A] Focus chain UB [auth D] Focus chain VA [auth A] Focus chain VB [auth E] Focus chain WA [auth A] Focus chain WB [auth F] Focus chain XA [auth A] 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 B] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth C] Focus chain LB [auth C] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PA [auth A] Focus chain PB [auth C] Focus chain QA [auth A] Focus chain QB [auth C] Focus chain RA [auth A] Focus chain RB [auth C] Focus chain SA [auth A] Focus chain SB [auth C] Focus chain TA [auth A] Focus chain TB [auth C] Focus chain UA [auth A] Focus chain UB [auth D] Focus chain VA [auth A] Focus chain VB [auth E] Focus chain WA [auth A] Focus chain WB [auth F] Focus chain XA [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 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

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

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: 2020-11-18
Type: Initial release
Version 1.1: 2020-12-02
Changes: Database references
Version 1.2: 2021-01-13
Changes: Database references
Version 2.0: 2021-02-10
Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-10-16
Changes: Data collection, Database references, Structure summary