7DWX

Conformation 1 of S-ACE2-B0AT1 ternary complex

PDB DOI: https://doi.org/10.2210/pdb7DWX/pdb
EM Map EMD-30888: EMDB EMDataResource

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

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: 8.30 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

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: 1,228.7 kDa
Atom Count: 71,532
Modelled Residue Count: 8,744
Deposited Residue Count: 10,640
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent neutral amino acid transporter B(0)AT1	A, C	654	Homo sapiens	Mutation(s): 0 Gene Names: SLC6A19, B0AT1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q695T7 (Homo sapiens) Explore Q695T7 Go to UniProtKB: Q695T7
PHAROS: Q695T7 GTEx: ENSG00000174358
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q695T7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	B, D	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) Membrane Entity: Yes
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	E, F, G, H, I E, F, G, H, I, J	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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
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], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], AA [auth a], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], CB [auth 2], DA [auth d], DB [auth 3], EA [auth e], EB [auth 4], FA [auth f], FB [auth 5], GA [auth g], GB [auth 6], HA [auth h], HB [auth 7], IA [auth i], IB [auth 8], JA [auth j], JB [auth 9], K, KA [auth k], KB [auth AA], L, LA [auth l], LB [auth BA], M, MA [auth m], MB [auth CA], N, NA [auth n], NB [auth DA], O, OA [auth o], OB [auth EA], P, PA [auth p], PB [auth FA], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain IB [auth 8] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain K Focus chain KA [auth k] Focus chain KB [auth AA] Focus chain L Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain M Focus chain MA [auth m] Focus chain MB [auth CA] Focus chain N Focus chain NA [auth n] Focus chain NB [auth DA] Focus chain O Focus chain OA [auth o] Focus chain OB [auth EA] Focus chain P Focus chain PA [auth p] Focus chain PB [auth FA] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FA [auth f] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HA [auth h] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain IB [auth 8] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain K Focus chain KA [auth k] Focus chain KB [auth AA] Focus chain L Focus chain LA [auth l] Focus chain LB [auth BA] Focus chain M Focus chain MA [auth m] Focus chain MB [auth CA] Focus chain N Focus chain NA [auth n] Focus chain NB [auth DA] Focus chain O Focus chain OA [auth o] Focus chain OB [auth EA] Focus chain P Focus chain PA [auth p] Focus chain PB [auth FA] Focus chain Q Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 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 AD [auth G] SDF format, chain AE [auth J] SDF format, chain BD [auth G] SDF format, chain CE [auth J] SDF format, chain EE [auth J] SDF format, chain FD [auth H] SDF format, chain GD [auth H] SDF format, chain JC [auth E] SDF format, chain LD [auth H] SDF format, chain MC [auth E] SDF format, chain OD [auth I] SDF format, chain PD [auth I] SDF format, chain RB [auth A] SDF format, chain RC [auth F] SDF format, chain UC [auth F] SDF format, chain WD [auth I] SDF format, chain XB [auth C] SDF format, chain YC [auth G] SDF format, chain YD [auth J] SDF format, chain AC [auth C] SDF format, chain BE [auth J] SDF format, chain CC [auth D] SDF format, chain CD [auth G] SDF format, chain DD [auth G] SDF format, chain DE [auth J] SDF format, chain EC [auth E] SDF format, chain ED [auth G] SDF format, chain FC [auth E] SDF format, chain FE [auth J] SDF format, chain GC [auth E] SDF format, chain HC [auth E] SDF format, chain HD [auth H] SDF format, chain IC [auth E] SDF format, chain ID [auth H] SDF format, chain JD [auth H] SDF format, chain KC [auth E] SDF format, chain KD [auth H] SDF format, chain LC [auth E] SDF format, chain MD [auth H] SDF format, chain NC [auth F] SDF format, chain ND [auth H] SDF format, chain OC [auth F] SDF format, chain PC [auth F] SDF format, chain QB [auth A] SDF format, chain QC [auth F] SDF format, chain QD [auth I] SDF format, chain RD [auth I] SDF format, chain SB [auth A] SDF format, chain SC [auth F] SDF format, chain SD [auth I] SDF format, chain TB [auth A] SDF format, chain TC [auth F] SDF format, chain TD [auth I] SDF format, chain UD [auth I] SDF format, chain VB [auth B] SDF format, chain VC [auth F] SDF format, chain VD [auth I] SDF format, chain WC [auth F] SDF format, chain XC [auth G] SDF format, chain XD [auth I] SDF format, chain YB [auth C] SDF format, chain ZB [auth C] SDF format, chain ZC [auth G] SDF format, chain ZD [auth J] MOL2 format, chain AD [auth G] MOL2 format, chain AE [auth J] MOL2 format, chain BD [auth G] MOL2 format, chain CE [auth J] MOL2 format, chain EE [auth J] MOL2 format, chain FD [auth H] MOL2 format, chain GD [auth H] MOL2 format, chain JC [auth E] MOL2 format, chain LD [auth H] MOL2 format, chain MC [auth E] MOL2 format, chain OD [auth I] MOL2 format, chain PD [auth I] MOL2 format, chain RB [auth A] MOL2 format, chain RC [auth F] MOL2 format, chain UC [auth F] MOL2 format, chain WD [auth I] MOL2 format, chain XB [auth C] MOL2 format, chain YC [auth G] MOL2 format, chain YD [auth J] MOL2 format, chain AC [auth C] MOL2 format, chain BE [auth J] MOL2 format, chain CC [auth D] MOL2 format, chain CD [auth G] MOL2 format, chain DD [auth G] MOL2 format, chain DE [auth J] MOL2 format, chain EC [auth E] MOL2 format, chain ED [auth G] MOL2 format, chain FC [auth E] MOL2 format, chain FE [auth J] MOL2 format, chain GC [auth E] MOL2 format, chain HC [auth E] MOL2 format, chain HD [auth H] MOL2 format, chain IC [auth E] MOL2 format, chain ID [auth H] MOL2 format, chain JD [auth H] MOL2 format, chain KC [auth E] MOL2 format, chain KD [auth H] MOL2 format, chain LC [auth E] MOL2 format, chain MD [auth H] MOL2 format, chain NC [auth F] MOL2 format, chain ND [auth H] MOL2 format, chain OC [auth F] MOL2 format, chain PC [auth F] MOL2 format, chain QB [auth A] MOL2 format, chain QC [auth F] MOL2 format, chain QD [auth I] MOL2 format, chain RD [auth I] MOL2 format, chain SB [auth A] MOL2 format, chain SC [auth F] MOL2 format, chain SD [auth I] MOL2 format, chain TB [auth A] MOL2 format, chain TC [auth F] MOL2 format, chain TD [auth I] MOL2 format, chain UD [auth I] MOL2 format, chain VB [auth B] MOL2 format, chain VC [auth F] MOL2 format, chain VD [auth I] MOL2 format, chain WC [auth F] MOL2 format, chain XC [auth G] MOL2 format, chain XD [auth I] MOL2 format, chain YB [auth C] MOL2 format, chain ZB [auth C] MOL2 format, chain ZC [auth G] MOL2 format, chain ZD [auth J]	AC [auth C] AD [auth G] AE [auth J] BD [auth G] BE [auth J] AC [auth C], AD [auth G], AE [auth J], BD [auth G], BE [auth J], CC [auth D], CD [auth G], CE [auth J], DD [auth G], DE [auth J], EC [auth E], ED [auth G], EE [auth J], FC [auth E], FD [auth H], FE [auth J], GC [auth E], GD [auth H], HC [auth E], HD [auth H], IC [auth E], ID [auth H], JC [auth E], JD [auth H], KC [auth E], KD [auth H], LC [auth E], LD [auth H], MC [auth E], MD [auth H], NC [auth F], ND [auth H], OC [auth F], OD [auth I], PC [auth F], PD [auth I], QB [auth A], QC [auth F], QD [auth I], RB [auth A], RC [auth F], RD [auth I], SB [auth A], SC [auth F], SD [auth I], TB [auth A], TC [auth F], TD [auth I], UC [auth F], UD [auth I], VB [auth B], VC [auth F], VD [auth I], WC [auth F], WD [auth I], XB [auth C], XC [auth G], XD [auth I], YB [auth C], YC [auth G], YD [auth J], ZB [auth C], ZC [auth G], ZD [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AC [auth C] Focus chain AD [auth G] Focus chain AE [auth J] Focus chain BD [auth G] Focus chain BE [auth J] Focus chain CC [auth D] Focus chain CD [auth G] Focus chain CE [auth J] Focus chain DD [auth G] Focus chain DE [auth J] Focus chain EC [auth E] Focus chain ED [auth G] Focus chain EE [auth J] Focus chain FC [auth E] Focus chain FD [auth H] Focus chain FE [auth J] Focus chain GC [auth E] Focus chain GD [auth H] Focus chain HC [auth E] Focus chain HD [auth H] Focus chain IC [auth E] Focus chain ID [auth H] Focus chain JC [auth E] Focus chain JD [auth H] Focus chain KC [auth E] Focus chain KD [auth H] Focus chain LC [auth E] Focus chain LD [auth H] Focus chain MC [auth E] Focus chain MD [auth H] Focus chain NC [auth F] Focus chain ND [auth H] Focus chain OC [auth F] Focus chain OD [auth I] Focus chain PC [auth F] Focus chain PD [auth I] Focus chain QB [auth A] Focus chain QC [auth F] Focus chain QD [auth I] Focus chain RB [auth A] Focus chain RC [auth F] Focus chain RD [auth I] Focus chain SB [auth A] Focus chain SC [auth F] Focus chain SD [auth I] Focus chain TB [auth A] Focus chain TC [auth F] Focus chain TD [auth I] Focus chain UC [auth F] Focus chain UD [auth I] Focus chain VB [auth B] Focus chain VC [auth F] Focus chain VD [auth I] Focus chain WC [auth F] Focus chain WD [auth I] Focus chain XB [auth C] Focus chain XC [auth G] Focus chain XD [auth I] Focus chain YB [auth C] Focus chain YC [auth G] Focus chain YD [auth J] Focus chain ZB [auth C] Focus chain ZC [auth G] Focus chain ZD [auth J] Interactions & Density Focus chain AC [auth C] Focus chain AD [auth G] Focus chain AE [auth J] Focus chain BD [auth G] Focus chain BE [auth J] Focus chain CC [auth D] Focus chain CD [auth G] Focus chain CE [auth J] Focus chain DD [auth G] Focus chain DE [auth J] Focus chain EC [auth E] Focus chain ED [auth G] Focus chain EE [auth J] Focus chain FC [auth E] Focus chain FD [auth H] Focus chain FE [auth J] Focus chain GC [auth E] Focus chain GD [auth H] Focus chain HC [auth E] Focus chain HD [auth H] Focus chain IC [auth E] Focus chain ID [auth H] Focus chain JC [auth E] Focus chain JD [auth H] Focus chain KC [auth E] Focus chain KD [auth H] Focus chain LC [auth E] Focus chain LD [auth H] Focus chain MC [auth E] Focus chain MD [auth H] Focus chain NC [auth F] Focus chain ND [auth H] Focus chain OC [auth F] Focus chain OD [auth I] Focus chain PC [auth F] Focus chain PD [auth I] Focus chain QB [auth A] Focus chain QC [auth F] Focus chain QD [auth I] Focus chain RB [auth A] Focus chain RC [auth F] Focus chain RD [auth I] Focus chain SB [auth A] Focus chain SC [auth F] Focus chain SD [auth I] Focus chain TB [auth A] Focus chain TC [auth F] Focus chain TD [auth I] Focus chain UC [auth F] Focus chain UD [auth I] Focus chain VB [auth B] Focus chain VC [auth F] Focus chain VD [auth I] Focus chain WC [auth F] Focus chain WD [auth I] Focus chain XB [auth C] Focus chain XC [auth G] Focus chain XD [auth I] Focus chain YB [auth C] Focus chain YC [auth G] Focus chain YD [auth J] Focus chain ZB [auth C] Focus chain ZC [auth G] Focus chain ZD [auth J]
LEU Query on LEU Download Ideal Coordinates CCD File SDF format, chain BC [auth C] SDF format, chain UB [auth A] MOL2 format, chain BC [auth C] MOL2 format, chain UB [auth A]	BC [auth C], UB [auth A]	LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-YFKPBYRVSA-N		Interactions Focus chain BC [auth C] Focus chain UB [auth A] Interactions & Density Focus chain BC [auth C] Focus chain UB [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain DC [auth D] SDF format, chain WB [auth B] MOL2 format, chain DC [auth D] MOL2 format, chain WB [auth B]	DC [auth D], WB [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DC [auth D] Focus chain WB [auth B] Interactions & Density Focus chain DC [auth D] Focus chain WB [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.30 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: 2021-03-31

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