Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 16-mer - A4B4C4D4 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 108826.80 
• Atom Count: 7543 
• Residue Count: 975 
• Unique protein chains: 4

2B4C

Crystal structure of HIV-1 JR-FL gp120 core protein containing the third variable region (V3) complexed with CD4 and the X5 antibody

• DOI: 10.2210/pdb2B4C/pdb

• Classification: Viral protein/Immune system
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Cricetulus griseus, Drosophila melanogaster, Escherichia coli


• Deposited: 2005-09-23 Released: 2005-11-15 
• Deposition Author(s): Huang, C., Tang, M., Zhang, M.Y., Majeed, S., Montabana, E., Stanfield, R.L., Dimitrov, D.S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.3 Å
• R-Value Free: 0.349 
• R-Value Work: 0.319 

Literature

Structure of a V3-containing HIV-1 gp120 core.

Huang, C.C., Tang, M., Zhang, M.Y., Majeed, S., Montabana, E., Stanfield, R.L., Dimitrov, D.S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P.D.

(2005) Science 310: 1025-1028

• PubMed: 16284180 
• DOI: 10.1126/science.1118398


• PubMed Abstract: 
  

The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor and to the X5 antibody at 3.5 angstrom resolution. Binding of gp120 to cell-surface CD4 would position V3 so that its coreceptor-binding tip protrudes 30 angstroms from the core toward the target cell membrane. The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization.

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Organizational Affiliation: 

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
envelope glycoprotein	G	344	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for Q75760 (Human immunodeficiency virus 1) Go to UniProtKB:  Q75760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
T-cell surface glycoprotein CD4	C	181	Homo sapiens	Mutation(s): 0  Gene Names: CD4
Find proteins for P01730 (Homo sapiens) Go to Gene View: CD4 Go to UniProtKB:  P01730

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
anti-HIV-1 gp120 immunoglobulin X5 light chain	L	215	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
anti-HIV-1 gp120 immunoglobulin X5 heavy chain	H	235	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	G, H, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FUC	G	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
XYL	H	D-XYLITOL C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N
NDG	G	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	G	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.3 Å
• R-Value Free: 0.349 
• R-Value Work: 0.319 
• Space Group: P 6 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 225.993	α = 90.00
b = 225.993	β = 90.00
c = 97.968	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-23 
• Released Date: 2005-11-15 
• Deposition Author(s): Huang, C., Tang, M., Zhang, M.Y., Majeed, S., Montabana, E., Stanfield, R.L., Dimitrov, D.S., Korber, B., Sodroski, J., Wilson, I.A., Wyatt, R., Kwong, P.D.

Revision History 

• Version 1.0: 2005-11-15
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2017-08-16
  Type: Refinement description, Source and taxonomy