Immunological Data Discovery Index
Immunological Data Discovery Index
| identifier: | 1969717 |
| description: |
epitope description:K248, V250, S252, E271, S274, D275, N276, A277, K278, S358, G359, G360, D361, I364, R447, D448, G449, G450, S456, R463, G466, G467, D468
antigen name:Envelope glycoprotein gp160
host organism:Homo sapiens
antibody name:VRC-PG04
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| aggregation: |
instance of dataset
|
| availability: |
available
|
| primaryPublications: |
23236069 |
| authorizations: |
registration not required
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| accessURL: |
http://www.iedb.org/reference/1025438 |
| landingPage: |
http://www.iedb.org/assay/1969717 |
| type: |
Literature
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| publicationVenue: |
J Virol
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| dates: |
2013
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| study type: | b cell assays |
| subject species: | Human immunodeficiency virus 1 |
| fullName: |
M Gordon Joyce
Masaru Kanekiyo
Ling Xu
Christian Biertü
mpfel
Jeffrey C Boyington
Stephanie Moquin
Wei Shi
Xueling Wu
Yongping Yang
Zhi-Yong Yang
Baoshan Zhang
Anqi Zheng
Tongqing Zhou
Jiang Zhu
John R Mascola
Peter D Kwong
Gary J Nabel
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| method: |
x-ray crystallography
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| name: |
Outer domain of HIV-1 gp120: antigenic optimization, structural malleability, and crystal structure with antibody VRC-PG04.
|
| description: |
The epitope residues were calculated from [PDB: 4I3R] as the antigen residues at 4Å
atomic distance from the antibody. Additional contact residues D276, N283, S460 and G461 were mismatched to residues N272, T279, N454 and N455, respectively, in the natural sequence in the GenBank entry. The epitope calculated from [PDB: 4I3S] is part of this epitope and includes the residues K252, E275, S278, D279, N280, A281, K282, S365, G366, G367, D368, I371, R456, D457, G458, G459, S462, R469, G472, G473. Additional contact residues D276 and S460 were mismatched to residues N272 and N454, respectively, in the natural sequence in the GenBank entry.
The epitope of VRC-PG04 Fab on the outer domain construct of HIV-1 gp120 (KER2018 Od4.2.2) was determined from the crystal structure of the complex, solved by molecular replacement. Two crystal forms of the complex were observed. This complex was space group P21 and the other form was space group P3221 [PDB: 4I3R]. The construct was based on the outer domain OD1 construct containing residues 252-482 of HIV-1 gp120 from a clade B R2 strain. The OD4.2.2 construct had residues substituted from the clade A KER2018 strain. Additional changes were introduced including mutation of N-linked and O-linked glycosylation sites, truncation of ß20-21 strands and V3 and V5 loops, and introduction of a disulfide bond to create a stable outer domain molecule with increased affinity for the antibody.
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| name: |
iedb
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| homePage: |
http://www.iedb.org |
