Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 93.50 kDa 
• Atom Count: 6790 
• Residue Count: 791 
• Unique protein chains: 2

6LZG

Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2

• DOI: 10.2210/pdb6LZG/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2020-02-19 Released: 2020-03-18 
• Deposition Author(s): Wang, Q.H., Song, H., Qi, J.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.

Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., Lu, G., Qiao, C., Hu, Y., Yuen, K.Y., Wang, Q., Zhou, H., Yan, J., Qi, J.

(2020) Cell 181: 894-904.e9

• PubMed: 32275855 
• DOI: 10.1016/j.cell.2020.03.045
• Primary Citation of Related Structures:  
  6LZG


• PubMed Abstract: 
  

The recent emergence of a novel coronavirus (SARS-CoV-2) in China has caused significant public health concerns. Recently, ACE2 was reported as an entry receptor for SARS-CoV-2. In this study, we present the crystal structure of the C-terminal domain of SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in complex with human ACE2 (hACE2), which reveals a hACE2-binding mode similar overall to that observed for SARS-CoV. However, atomic details at the binding interface demonstrate that key residue substitutions in SARS-CoV-2-CTD slightly strengthen the interaction and lead to higher affinity for receptor binding than SARS-RBD. Additionally, a panel of murine monoclonal antibodies (mAbs) and polyclonal antibodies (pAbs) against SARS-CoV-S1/receptor-binding domain (RBD) were unable to interact with the SARS-CoV-2 S protein, indicating notable differences in antigenicity between SARS-CoV and SARS-CoV-2. These findings shed light on the viral pathogenesis and provide important structural information regarding development of therapeutic countermeasures against the emerging virus.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	596	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 protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Solute Carrier (SLC) Transporter Superfamily	Protein:  Coronavirus spike receptor-binding domain complexed with ACE2
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
NIH Common Fund Data Resources
PHAROS  Q9BYF1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	209	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Solute Carrier (SLC) Transporter Superfamily	Protein:  Coronavirus spike receptor-binding domain complexed with ACE2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.448	α = 90
b = 104.448	β = 90
c = 229.786	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data processing
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-02-19 
• Released Date: 2020-03-18 
Deposition Author(s): Wang, Q.H., Song, H., Qi, J.X.

Revision History 

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Structure summary
• Version 2.0: 2020-04-22
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Database references, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.2: 2020-05-27
  Changes: Database references
• Version 2.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary