FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170)


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B-Cell Epitope
Epitope  
   
Complex PDB ID 1A3R
Accession Number 3DIEP0003
IEDB ID 69178
Epitope Sequence VKAETRLNPDLQPTE
Starting Position156
Ending Position170
Epitope Type Linear Epitope

Assay Information  
Assay Antigen VKAETRLNPDLQPTE Chain 2; Human Rhinovirus Serotype 2 (Hrv2) (156-170) Human rhinovirus 2
PDB CategoryViral protein/Immune system
Keyword IMMUNOGLOBULIN; ANTIBODY; RHINOVIRUS; NEUTRALIZATION; CONTINUOUS EPITOPE; COMPLEX (IMMUNOGLOBULIN/VIRAL PEPTIDE); Viral protein/Immune system COMPLEX
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain H
Antibody Chain 2 PDB ChainL
Antigen PDB ChainP
Contact Area for Antigen 1098.2
Contact Area for Antibody867.2
CommentsResidues between A158 and D165 (AETRLNPD) provide the greatest contribution to the contact surface area; consistent with definition of the minimal binding site (TRLNPD) by epitope mapping. The peptide has a compact folded conformation with a ?-turn between Ala158 and Thr160; a short 3-10 helix formed by the residues Pro164 - Gln167 and the hydrogen bonds between Asn163 and Asp165 and between Gln167 and Glu170 and a salt bridge between Glu159 and Arg161. Pro168 is in cis conformation. All the peptide residues directly interact with the Fab. The peptide residues K157-P164 can be superimposed with the corresponded residues from HRV1A intact virion [PDB:1R1A]; which is closely related to HRV2; at r.m.s. of 0.9 Ã… for Ca atoms. The 8F5 Fab (anliganded structure is [PDB:1BBD]) undergoes significant conformational changes upon the peptide binding (the details are provided in the paper). .

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.1
R-Value
0.171
Space Group
P 21 21 21
Unit Cell
Length(Å) Angle(°)
a = 71.79 α = 90
b = 76.32 β = 90
c = 92.32 γ = 90


Source Information  
Structure Determination Method X-RAY DIFFRACTION
Source Organism Mus musculus
Common Namehouse mouse
Taxonomic ID10090
Source Organism Mus musculus
Common Namehouse mouse
Taxonomic ID10090
Source Organism Human rhinovirus 2
Taxonomic ID12130
Entity ID3

Ligand non-polymer
Ligand NameAMINO GROUP
Chem Name NH2




Sequence
Protein Name
AMINO GROUP
Poly type
polypeptide(L)
Sequence status
Complete

Err:Conn