PDBsum entry 4zto

Immune system

PDB id: 4zto

Contents

Protein chains

216 a.a.

221 a.a.

11 a.a.

Ligands

GLY-LYS-ALA-MET-TYR-ALA-PRO-PRO-ILE-ARG

Waters ×988

PDB id:

4zto

Name:

Immune system

Title:

Fab/epitope complex structure of rabbit monoclonal antibody r53 targeting an epitope in HIV-1 gp120 c4 region

Structure:

Rabbit monoclonal antibody r53 fab light chain. Chain: l, m. Engineered: yes. Rabbit monoclonal antibody r53 fab heavy chain. Chain: h, i. Engineered: yes. Epitope of rabbit monoclonal antibody r53. Chain: p, q. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Expressed in: homo sapiens. Expression_system_taxid: 9606. Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676

Resolution:

2.30Å R-factor: 0.170 R-free: 0.223

Authors:

R.Pan,X.-P.Kong

Key ref:

R.Pan et al. (2015). Structural analysis of a novel rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region critical for receptor and co-receptor binding. Emerg Microbes Infect, 4, e44. PubMed id: 26251831 DOI: 10.1038/emi.2015.44

Date:

14-May-15 Release date: 19-Aug-15

Protein chains

No UniProt id for this chain

Struc: 216 a.a.

Protein chains

No UniProt id for this chain

Struc: 221 a.a.

Protein chain

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

Seq: 856 a.a.

Struc: 11 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1038/emi.2015.44

Emerg Microbes Infect 4:e44 (2015)

PubMed id: 26251831

Structural analysis of a novel rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region critical for receptor and co-receptor binding.

R.Pan, Y.Chen, M.Vaine, G.Hu, S.Wang, S.Lu, X.P.Kong.

ABSTRACT

The fourth conserved region (C4) in the HIV-1 envelope glycoprotein (Env) gp120 is a structural element that is important for its function, as it binds to both the receptor CD4 and the co-receptor CCR5/CXCR4. It has long been known that this region is highly immunogenic and that it harbors B-cell as well as T-cell epitopes. It is the target of a number of antibodies in animal studies, which are called CD4-blockers. However, the mechanism by which the virus shields itself from such antibody responses is not known. Here, we determined the crystal structure of R53 in complex with its epitope peptide using a novel anti-C4 rabbit monoclonal antibody R53. Our data show that although the epitope of R53 covers a highly conserved sequence (433)AMYAPPI(439), it is not available in the gp120 trimer and in the CD4-bound conformation. Our results suggest a masking mechanism to explain how HIV-1 protects this critical region from the human immune system.