2H32

Crystal structure of the pre-B cell receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.1139412
  • Primary Citation of Related Structures:  

  • 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" ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin iota chain
A
126Homo sapiensMutation(s): 0 
Gene Names: VPREB1 (VPREB)
Find proteins for P12018 (Homo sapiens)
Go to Gene View: VPREB1
Go to UniProtKB:  P12018
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin omega chain
B
121Homo sapiensMutation(s): 0 
Gene Names: IGLL1 (IGL1)
Find proteins for P15814 (Homo sapiens)
Go to Gene View: IGLL1
Go to UniProtKB:  P15814
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin heavy chain
H
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.267 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.502α = 90.00
b = 71.502β = 90.00
c = 217.932γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
ADSCdata collection
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-05-22 
  • Released Date: 2007-04-24 
  • Deposition Author(s): Bankovich, A.J.

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance