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 and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 182.06 kDa 
• Atom Count: 12777 
• Residue Count: 1542 
• Unique protein chains: 2

2AJF

Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor

• DOI: 10.2210/pdb2AJF/pdb

• Classification: hydrolase/viral protein
• Organism(s): Homo sapiens, Severe acute respiratory syndrome-related coronavirus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-08-01 Released: 2005-09-20 
• Deposition Author(s): Li, F., Li, W., Farzan, M., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Literature

Structure of SARS coronavirus spike receptor-binding domain complexed with receptor.

Li, F., Li, W., Farzan, M., Harrison, S.C.

(2005) Science 309: 1864-1868

• PubMed: 16166518 
• DOI: 10.1126/science.1116480
• Primary Citation of Related Structures:  
  2AJF


• PubMed Abstract: 
  

The spike protein (S) of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). A defined receptor-binding domain (RBD) on S mediates this interaction. The crystal structure at 2.9 angstrom resolution of the RBD bound with the peptidase domain of human ACE2 shows that the RBD presents a gently concave surface, which cradles the N-terminal lobe of the peptidase. The atomic details at the interface between the two proteins clarify the importance of residue changes that facilitate efficient cross-species infection and human-to-human transmission. The structure of the RBD suggests ways to make truncated disulfide-stabilized RBD variants for use in the design of coronavirus vaccines.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Laboratory of Molecular Medicine, 320 Longwood Avenue, Boston, MA 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme-Related Carboxypeptidase (Ace2)	A, B	597	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17 (PDB Primary Data), 3.4.17.23 (UniProt)
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
SARS-coronavirus spike protein	E, F	180	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: S, 2
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594  Go to UniProtKB:  P59594

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.299	α = 90
b = 119.429	β = 91.97
c = 113.237	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-01 
• Released Date: 2005-09-20 
Deposition Author(s): Li, F., Li, W., Farzan, M., Harrison, S.C.

Revision History 

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary