PDBsum entry 3j70

Viral protein/immune system

PDB id: 3j70

Contents

Protein chains

212 a.a.

210 a.a.

181 a.a.

470 a.a.

77 a.a.

PDB id:

3j70

Name:

Viral protein/immune system

Title:

Model of gp120, including variable regions, in complex with cd4 and 17b

Structure:

Monoclonal antibody 17b light chain. Chain: a, m, r. Monoclonal antibody 17b heavy chain. Chain: b, n, s. T-cell surface glycoprotein cd4. Chain: c, o, t. Fragment: unp residues 26-208. Synonym: t-cell surface antigen t4/leu-3. Envelope glycoprotein gp120.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Human immunodeficiency virus 1. HIV-1. Organism_taxid: 11676. Organism_taxid: 11676

Authors:

M.Rasheed,R.Bettadapura,C.Bajaj

Key ref:

M.Rasheed et al. (2015). Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State. Structure, 23, 1138-1149. PubMed id: 26039348 DOI: 10.1016/j.str.2015.03.026

Date:

22-Apr-14 Release date: 26-Aug-15

Protein chains

No UniProt id for this chain

Struc: 212 a.a.

Protein chains

No UniProt id for this chain

Struc: 210 a.a.

Protein chains

P01730  (CD4_HUMAN) -  T-cell surface glycoprotein CD4 from Homo sapiens

Seq: 458 a.a.

Struc: 181 a.a.

Protein chains

P04578  (ENV_HV1H2) -  Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 856 a.a.

Struc: 470 a.a.

Protein chains

No UniProt id for this chain

Struc: 77 a.a.

DOI no: 10.1016/j.str.2015.03.026

Structure 23:1138-1149 (2015)

PubMed id: 26039348

Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State.

M.Rasheed, R.Bettadapura, C.Bajaj.

ABSTRACT

Envelope glycoprotein gp120 of HIV-1 possesses several variable regions; their precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and 17b, complete with its variable regions. The model was produced by a computational protocol that uses cryo-electron microscopy (EM) maps, atomic-resolution structures of the core, and information on binding interactions. Our model has excellent fit with EMD: 5020, is stereochemically and energetically favorable, and has the expected binding interfaces. Comparison of the ternary arrangement of the loops in this model with those bound to PGT122 and PGV04 suggested a possible motion of the V1V2 away from the CCR5 binding site and toward CD4. Our study also revealed that the CD4-bound state of the V1V2 loop is not optimal for gp120 bound with several neutralizing antibodies.