2H32

Crystal structure of the pre-B cell receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.269 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Insight into Pre-B Cell Receptor Function

Bankovich, A.J.Raunser, S.Juo, Z.S.Walz, T.Davis, M.M.Garcia, K.C.

(2007) Science 316: 291-294

  • DOI: https://doi.org/10.1126/science.1139412
  • Primary Citation of Related Structures:  
    2H32, 2H3N

  • PubMed Abstract: 

    The pre-B cell receptor (pre-BCR) serves as a checkpoint in B cell development. In the 2.7 angstrom structure of a human pre-BCR Fab-like fragment, consisting of an antibody heavy chain (HC) paired with the surrogate light chain, the "unique regions" of VpreB and lambda5 replace the complementarity-determining region 3 (CDR3) loop of an antibody light chain and appear to "probe" the HC CDR3, potentially influencing the selection of the antibody repertoire. Biochemical analysis indicates that the pre-BCR is impaired in its ability to recognize antigen, which, together with electron microscopic visualization of a pre-BCR dimer, suggests ligand-independent oligomerization as the likely signaling mechanism.


  • Organizational Affiliation

    Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin iota chain126Homo sapiensMutation(s): 0 
Gene Names: VPREB1VPREB
UniProt & NIH Common Fund Data Resources
Find proteins for P12018 (Homo sapiens)
Explore P12018 
Go to UniProtKB:  P12018
PHAROS:  P12018
GTEx:  ENSG00000169575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12018
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin omega chain121Homo sapiensMutation(s): 0 
Gene Names: IGLL1IGL1
UniProt & NIH Common Fund Data Resources
Find proteins for P15814 (Homo sapiens)
Explore P15814 
Go to UniProtKB:  P15814
PHAROS:  P15814
GTEx:  ENSG00000128322 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15814
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin heavy chainC [auth H]223Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.269 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.502α = 90
b = 71.502β = 90
c = 217.932γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
CNSrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description