Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1BCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 106.80 kDa 
• Atom Count: 7877 
• Residue Count: 920 
• Unique protein chains: 4

1GC1

HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY

• DOI: 10.2210/pdb1GC1/pdb

• Classification: Viral protein/receptor/Immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Drosophila melanogaster, Cricetulus griseus, Mus musculus
• Mutation(s): Yes 


• Deposited: 1998-06-15 Released: 1998-07-08 
• Deposition Author(s): Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.302 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.

Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

(1998) Nature 393: 648-659

• PubMed: 9641677 
• DOI: 10.1038/31405
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The entry of human immunodeficiency virus (HIV) into cells requires the sequential interaction of the viral exterior envelope glycoprotein, gp120, with the CD4 glycoprotein and a chemokine receptor on the cell surface. These interactions initiate a fusion of the viral and cellular membranes. Although gp120 can elicit virus-neutralizing antibodies, HIV eludes the immune system. We have solved the X-ray crystal structure at 2.5 A resolution of an HIV-1 gp120 core complexed with a two-domain fragment of human CD4 and an antigen-binding fragment of a neutralizing antibody that blocks chemokine-receptor binding. The structure reveals a cavity-laden CD4-gp120 interface, a conserved binding site for the chemokine receptor, evidence for a conformational change upon CD4 binding, the nature of a CD4-induced antibody epitope, and specific mechanisms for immune evasion. Our results provide a framework for understanding the complex biology of HIV entry into cells and should guide efforts to intervene.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ENVELOPE PROTEIN GP120	G	321	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578  Go to UniProtKB:  P04578

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
CD4	C	185	Homo sapiens	Mutation(s): 2  Gene Names: CD4
Find proteins for P01730 (Homo sapiens) Explore P01730  Go to UniProtKB:  P01730
NIH Common Fund Data Resources
PHAROS  P01730 GTEx  ENSG00000010610

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
ANTIBODY 17B	H	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
ANTIBODY 17B	L	213	Homo sapiens	Mutation(s): 0

Oligosaccharides

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	A, B, D, E	2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.302 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.64	α = 90
b = 88.13	β = 90
c = 196.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-15 
• Released Date: 1998-07-08 
Deposition Author(s): Kwong, P.D., Wyatt, R., Robinson, J., Sweet, R.W., Sodroski, J., Hendrickson, W.A.

Revision History 

• Version 1.0: 1998-07-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2013-09-18
  Changes: Derived calculations
• Version 1.4: 2017-06-28
  Changes: Database references, Other, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary