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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.349 (Depositor), 0.310 (DCC)
R-Value Work:
0.319 (Depositor), 0.280 (DCC)
R-Value Observed:
0.319 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

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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 type 1) Explore Q75760 Go to UniProtKB: Q75760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q75760
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence LOADING

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01730
Sequence Annotations Expand
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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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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	Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

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 F [auth G] SDF format, chain G SDF format, chain H [auth G] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] mmCIF format, chain F [auth G] mmCIF format, chain G mmCIF format, chain H [auth G]	F [auth G], G, H [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth G] Focus chain G Focus chain H [auth G] Interactions & Density Focus chain F [auth G] Focus chain G Focus chain H [auth G]
XYL Query on XYL Download Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain M [auth H] SDF format, chain L [auth H] MOL2 format, chain K [auth H] MOL2 format, chain M [auth H] MOL2 format, chain L [auth H] mmCIF format, chain K [auth H] mmCIF format, chain M [auth H] mmCIF format, chain L [auth H]	K [auth H], L [auth H], M [auth H]	Xylitol C₅ H₁₂ O₅ HEBKCHPVOIAQTA-SCDXWVJYSA-N		Interactions Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Interactions & Density Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth G] SDF format, chain J [auth L] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] MOL2 format, chain I [auth G] MOL2 format, chain J [auth L] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] mmCIF format, chain I [auth G] mmCIF format, chain J [auth L] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H]	I [auth G], J [auth L], N [auth H], O [auth H], P [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth G] Focus chain J [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Interactions & Density Focus chain I [auth G] Focus chain J [auth L] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.349 (Depositor), 0.310 (DCC)
R-Value Work: 0.319 (Depositor), 0.280 (DCC)
R-Value Observed: 0.319 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-11-15

Deposition Author(s):

Revision History (Full details and data files)

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