5CAY | pdb_00005cay

Envelope glycoprotein gp120 core from HIV type 2 bound to the first two domains of human soluble CD4 receptor

• PDB DOI: https://doi.org/10.2210/pdb5CAY/pdb

• Classification: Viral Protein/immune System
• Organism(s): Human immunodeficiency virus type 2 (ISOLATE ST), Homo sapiens
• Expression System: Homo sapiens, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-06-30 Released: 2015-12-09 
• Deposition Author(s): Davenport, Y.W., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.287 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Models: experimental

Literature

Structure of an HIV-2 gp120 in Complex with CD4.

Davenport, Y.W., West, A.P., Bjorkman, P.J.

(2015) J Virol 90: 2112-2118

• PubMed: 26608312 
• DOI: https://doi.org/10.1128/JVI.02678-15
• Primary Citation Related Structures: 
  5CAY


• PubMed Abstract: 
  

  HIV-2 is a nonpandemic form of the virus causing AIDS, and the majority of HIV-2-infected patients exhibit long-term nonprogression. The HIV-1 and HIV-2 envelope glycoproteins, the sole targets of neutralizing antibodies, share 30 to 40% identity. As a first step in understanding the reduced pathogenicity of HIV-2, we solved a 3.0-Å structure of an HIV-2 gp120 bound to the host receptor CD4, which reveals structural similarity to HIV-1 gp120 despite divergence in amino acid sequence.

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Organizational Affiliation: 
• Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.97 kDa 
• Atom Count: 3,859 
• Modeled Residue Count: 461 
• Deposited Residue Count: 535 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120 core from ST strain of HIV-2	A [auth G]	345	Human immunodeficiency virus type 2 (ISOLATE ST)	Mutation(s): 0
UniProt
Find proteins for P20872 (Human immunodeficiency virus type 2 subtype A (isolate ST)) Explore P20872  Go to UniProtKB:  P20872
Glycosylation
Glycosylation Sites: 7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	B	190	Homo sapiens	Mutation(s): 0  Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730  Go to UniProtKB:  P01730
PHAROS:  P01730 GTEx:  ENSG00000010610

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	D [auth C]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth G], F [auth G], G, H [auth G], I [auth G], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.287 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.276	α = 90
b = 100.223	β = 90
c = 199.139	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Davenport, Y.W., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	8 DP1 DA035082-03
Bill & Melinda Gates Foundation	United States	OPP1040753

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary