1RVF | pdb_00001rvf

FAB COMPLEXED WITH INTACT HUMAN RHINOVIRUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Work: 
    0.212 (Depositor) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon.

Smith, T.J.Chase, E.S.Schmidt, T.J.Olson, N.H.Baker, T.S.

(1996) Nature 383: 350-354

  • DOI: https://doi.org/10.1038/383350a0
  • Primary Citation Related Structures: 
    1RVF

  • PubMed Abstract: 

    The three-dimensional structure of intact human rhinovirus 14 (HRV-14) complexed with Fab fragments (Fab17-IA) from a strongly neutralizing antibody that binds bivalently to the virion has been determined to 4.0 angstrom resolution by a combination of X-ray crystallography and cryo-electron microscopy. In contradiction to the most commonly held model of antibody-mediated neutralization, Fab17-IA does not induce a conformational change in the HRV-14 capsid. Instead, the paratope of the antibody undergoes a large conformational change to accommodate the epitope. Unlike any previously described antibody-antigen structure, the conserved framework region of the antibody makes extensive contact with the viral surface. Fab17-IA penetrates deep within the canyon in which the cellular receptor for HRV-14 binds. Hence, it is unlikely that viral quaternary structure evolves merely to evade immune recognition. Instead, the shape and position of the receptor-binding region on a virus probably dictates receptor binding and subsequent uncoating events and has little or no influence on concealing the virus from the immune system.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA. tom@bragg.bio.purdue.edu

Macromolecule Content 

  • Total Structure Weight: 119.37 kDa 
  • Atom Count: 8,019 
  • Modeled Residue Count: 1,033 
  • Deposited Residue Count: 1,084 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEINA [auth 1]289rhinovirus B14Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups
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UniProt GroupP03303
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEINB [auth 2]262rhinovirus B14Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups
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UniProt GroupP03303
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEINC [auth 3]236rhinovirus B14Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Entity Groups
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UniProt GroupP03303
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
HUMAN RHINOVIRUS 14 COAT PROTEIND [auth 4]68Human rhinovirus sp.Mutation(s): 0 
UniProt
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
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UniProt GroupP03303
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB 17-IAE [auth L]110Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8K1F2 (Mus musculus)
Explore Q8K1F2 
Go to UniProtKB:  Q8K1F2
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UniProt GroupQ8K1F2
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB 17-IAF [auth H]119Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Work:  0.212 (Depositor) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: R 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 372α = 108.4
b = 372β = 108.4
c = 372γ = 108.4
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
ENVELOPEmodel building
X-PLORrefinement
ENVELOPEphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 1998-02-25 
  • Deposition Author(s): Smith, T.J.

Revision History  (Full details and data files)

  • Version 1.0: 1998-02-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary