4I0K

Crystal structure of murine B7-H3 extracellular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report



Literature

Structure and T cell inhibition properties of B7 family member, B7-H3.

Vigdorovich, V.Ramagopal, U.A.Lazar-Molnar, E.Sylvestre, E.Lee, J.S.Hofmeyer, K.A.Zang, X.Nathenson, S.G.Almo, S.C.

(2013) Structure 21: 707-717

  • DOI: 10.1016/j.str.2013.03.003
  • Primary Citation of Related Structures:  
    4I0K

  • PubMed Abstract: 
  • T cell activity is controlled by a combination of antigen-dependent signaling through the T cell receptor and a set of auxiliary signals delivered through antigen-independent interactions, including the recognition of the B7 family of ligands. B7-H3 ...

    T cell activity is controlled by a combination of antigen-dependent signaling through the T cell receptor and a set of auxiliary signals delivered through antigen-independent interactions, including the recognition of the B7 family of ligands. B7-H3 is a recently identified B7 family member that is strongly overexpressed in a range of cancers and correlates with poor prognosis. We report the crystal structure of murine B7-H3 at a 3 Å resolution, which provides a model for the organization of the IgV and IgC domains within the ectodomain. We demonstrate that B7-H3 inhibits T cell proliferation and show that the FG loop of the IgV domain plays a critical role in this function. B7-H3 crystallized as an unusual dimer arising from the exchange of the G strands in the IgV domains of partner molecules. This arrangement, in combination with previous reports, highlights the dynamic nature and plasticity of the immunoglobulin fold.


    Organizational Affiliation

    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. vladimir.vigdorovich@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CD276 antigenA222Mus musculusMutation(s): 0 
Gene Names: B7-H3B7h3Cd276
Find proteins for Q8VE98 (Mus musculus)
Explore Q8VE98 
Go to UniProtKB:  Q8VE98
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.92α = 90
b = 100.92β = 90
c = 188.18γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
MOSFLMdata reduction
BALBESphasing

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary