RCSB Protein Data Bank - RCSB PDB - 2B4C Structure Summary

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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

2B4C

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Primary Citation

Related Citations in PDB Entry (REMARK 1) Hide

Molecular Description

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Classification:	Viral Protein/immune System
Structure Weight:	108809.71

Molecule:

envelope glycoprotein

Polymer:

Type:

protein

Length:

344

Chains:

Fragment:

CORE with V3

Mutation:

N301Q, T389A

Organism

Human immunodeficiency virus 1

Gene Name

env

UniProtKB:

| | Q75760

Molecule:

T-cell surface glycoprotein CD4

Polymer:

Type:

protein

Length:

181

Chains:

Fragment:

D1D2, N-TERMINAL TWO DOMAIN FRAGMENT

Organism

Homo sapiens

Gene Name

CD4

UniProtKB:

| | P01730

Molecule:

anti-HIV-1 gp120 immunoglobulin X5 light chain

Polymer:

Type:

protein

Length:

215

Chains:

Organism

Homo sapiens

Molecule:

anti-HIV-1 gp120 immunoglobulin X5 heavy chain

Polymer:

Type:

protein

Length:

235

Chains:

Organism

Homo sapiens

Source

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Polymer: 1

Scientific Name:

Human immunodeficiency virus 1

Taxonomy

Expression System:

Drosophila melanogaster

Polymer: 2

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Cricetulus griseus

Polymer: 3

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Escherichia coli

Polymer: 4

Scientific Name:

Homo sapiens

Taxonomy

Common Name:

Human

Expression System:

Escherichia coli

Polymer: 6

Scientific Name:

Synthetic construct

Taxonomy

Ligand Chemical Component

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Identifier	Formula	Name	Interactions
FUC Search Download	C₆ H₁₂ O₅	ALPHA-L-FUCOSE		Ligand Explorer
NAG Search Download	C₈ H₁₅ N O₆	N-ACETYL-D-GLUCOSAMINE		Ligand Explorer
NDG Search Download	C₈ H₁₅ N O₆	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE		Ligand Explorer
SO4 Search Download	O₄ S	SULFATE ION		Ligand Explorer
XYL Search Download	C₅ H₁₂ O₅	D-XYLITOL		Ligand Explorer

External Domain Annotations Hide
SCOP Classification v1.75: 7 Domains - data from SCOP

CATH Classification v3.4.0: 7 Domains - data from CATH

Pfam Classification: 16 Domains - data from Pfam
Structural Biology Knowledgebase Data Hide

Data in orange boxes are gathered from external resources (when available).

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Biological Assembly 1

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Biological assembly 1 assigned by authors

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Deposition Summary

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Authors: 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.

Deposition:	2005-09-23
Release:	2005-11-15
Last Modified (REVDAT):	2011-07-13

Revision History Hide

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2011-07-13
Version format compliance

2011-07-13
Biological assembly

Experimental Details

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Method: X-RAY DIFFRACTION
Exp. Data:
Structure Factors
EDS

Unit Cell:
	Length [Å]	Angles [°]
	a = 225.99	α = 90.00
	b = 225.99	β = 90.00
	c = 97.97	γ = 120.00

Molecule of the Month Hide
Epidermal Growth Factor

Nanobodies

Antibodies

T-Cell Receptor

Hemagglutinin