3QNZ

Orthorhombic form of IgG1 Fab fragment (in complex with antigenic tubulin peptide) sharing same Fv as IgA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a human IgA1 Fab fragment at 1.55 angstrom resolution: potential effect of the constant domains on antigen-affinity modulation

Correa, A.Trajtenberg, F.Obal, G.Pritsch, O.Dighiero, G.Oppezzo, P.Buschiazzo, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 388-397

  • DOI: https://doi.org/10.1107/S0907444912048664
  • Primary Citation of Related Structures:  
    3M8O, 3QNX, 3QNY, 3QNZ, 3QO1

  • PubMed Abstract: 

    Despite being the most abundant class of immunoglobulins in humans and playing central roles in the adaptive immune response, high-resolution structural data are still lacking for the antigen-binding region of human isotype A antibodies (IgAs). The crystal structures of a human Fab fragment of IgA1 in three different crystal forms are now reported. The three-dimensional organization is similar to those of other Fab classes, but FabA1 seems to be more rigid, being constrained by a hydrophobic core in the interface between the variable and constant domains of the heavy chain (VH-CH1) as well as by a disulfide bridge that connects the light and heavy chains, influencing the relative heavy/light-chain orientation. The crystal structure of the same antibody but with a G-isotype CH1 which is reported to display different antigen affinity has also been solved. The differential structural features reveal plausible mechanisms for constant/variable-domain long-distance effects whereby antibody class switching could alter antigen affinity.


  • Organizational Affiliation

    Unit of Recombinant Proteins, Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment of IMMUNOGLOBULIN G1 LIGHT CHAIN219Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment of IMMUNOGLOBULIN G1 HEAVY CHAIN220Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
peptide from Tubulin beta chain10N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07437 (Homo sapiens)
Explore P07437 
Go to UniProtKB:  P07437
PHAROS:  P07437
GTEx:  ENSG00000196230 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07437
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.37α = 90
b = 66.45β = 90
c = 137.68γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2014-03-05
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description