2B4C

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

• PDB DOI: https://doi.org/10.2210/pdb2B4C/pdb

• Classification: Viral protein/Immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Drosophila melanogaster, Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• 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: 3.30 Å
• R-Value Free: 0.349 
• R-Value Work: 0.319 
• R-Value Observed: 0.319 

Starting Models: experimental

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: https://doi.org/10.1126/science.1118398
• Primary Citation of Related Structures:  
  2B4C


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 108.81 kDa 
• Atom Count: 7,543 
• Modelled Residue Count: 962 
• Deposited Residue Count: 975 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope glycoprotein	A [auth G]	344	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q75760 (Human immunodeficiency virus 1) Go to UniProtKB:  Q75760
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD4	B [auth C]	181	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-HIV-1 gp120 immunoglobulin X5 light chain	C [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-HIV-1 gp120 immunoglobulin X5 heavy chain	D [auth H]	235	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth G], G, H [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
XYL	K [auth H], L [auth H], M [auth H]	Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N
SO4	I [auth G], J [auth L], N [auth H], O [auth H], P [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.349 
• R-Value Work: 0.319 
• R-Value Observed: 0.319 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 225.993	α = 90
b = 225.993	β = 90
c = 97.968	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-08-16
  Changes: Refinement description, 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
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary