6M18 | pdb_00006m18

ACE2-B0AT1 complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6M18

This is version 3.1 of the entry. See complete history. 

Literature

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.

Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., Zhou, Q.

(2020) Science 367: 1444-1448

  • DOI: https://doi.org/10.1126/science.abb2762
  • Primary Citation Related Structures: 
    6M17, 6M18, 6M1D

  • PubMed Abstract: 

    Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious coronavirus disease 2019 (COVID-19) epidemic. Here, we present cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B 0 AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 angstroms at the ACE2-RBD interface. The ACE2-B 0 AT1 complex is assembled as a dimer of heterodimers, with the collectrin-like domain of ACE2 mediating homodimerization. The RBD is recognized by the extracellular peptidase domain of ACE2 mainly through polar residues. These findings provide important insights into the molecular basis for coronavirus recognition and infection.

    • Organizational Affiliation: 
    • Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.

Macromolecule Content 

  • Total Structure Weight: 345.2 kDa 
  • Atom Count: 22,534 
  • Modeled Residue Count: 2,708 
  • Deposited Residue Count: 2,936 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium-dependent neutral amino acid transporter B(0)AT1
A, C
654Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ695T7
Glycosylation
Glycosylation Sites: 5
Go to GlyGen: Q695T7-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2
B, D
814Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 7
Go to GlyGen: Q9BYF1-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PH
(Subject of Investigation/LOI)

Query on 3PH


Download:Ideal Coordinates CCD File
EA [auth C],
FA [auth C],
W [auth A],
X [auth A]		1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
NAG
(Subject of Investigation/LOI)

Query on NAG


Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
GA [auth D]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
GA [auth D],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN


Download:Ideal Coordinates CCD File
HA [auth D],
Z [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.6

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971123
National Natural Science Foundation of China (NSFC)China81920108015
National Natural Science Foundation of China (NSFC)China31930059

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-04-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2020-11-04
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary