2AJF | pdb_00002ajf

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.275 (Depositor), 0.305 (DCC)
R-Value Work:
0.218 (Depositor)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1126/science.1116480
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 182.06 kDa
Atom Count: 12,777
Modeled Residue Count: 1,542
Deposited Residue Count: 1,554
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 EC: 3.4.17 (PDB Primary Data), 3.4.17.23 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-coronavirus spike protein	C [auth E], D [auth F]	180	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 Gene Names: S
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594 Go to UniProtKB: P59594
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59594
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth E] Focus chain D [auth F]	Go to GlyGen: P59594-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], F [auth D]	3		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth B] O [auth E] G [auth A], H [auth A], I [auth A], L [auth B], O [auth E], P [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth E] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth E] Focus chain P [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	K [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.275 (Depositor), 0.305 (DCC)
R-Value Work: 0.218 (Depositor)
R-Value Observed: 0.221 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-09-20

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.0: 2024-12-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary