6M17

The 2019-nCoV RBD/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


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 of 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 ...

    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: 

    School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium-dependent neutral amino acid transporter B(0)AT1A,
D [auth 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ695T7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2B,
E [auth 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
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UniProt GroupQ9BYF1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1C [auth E],
F		223Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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  
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UniProt GroupP0DTC2
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K, L, M, O, P, Q, R, S, T, U
G, H, I, J, K, L, M, O, P, Q, R, S, T, U
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN, V 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
BA [auth B],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
BA [auth B],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
IA [auth D],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
LEU (Subject of Investigation/LOI)
Query on LEU
Download Ideal Coordinates CCD File 
AA [auth A],
HA [auth C]		LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N		 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
CA [auth B],
JA [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.13.2

Structure Validation

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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: 2020-04-01
    Changes: Source and taxonomy, Structure summary
  • Version 1.3: 2020-04-08
    Changes: Database references
  • Version 1.4: 2020-04-29
    Changes: Structure summary
  • Version 1.5: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • 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: Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2021-03-10
    Changes: Structure summary