4I0K | pdb_00004i0k

Crystal structure of murine B7-H3 extracellular domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 
    0.250 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history

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: https://doi.org/10.1016/j.str.2013.03.003
  • Primary Citation 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 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

Macromolecule Content 

  • Total Structure Weight: 25.43 kDa 
  • Atom Count: 1,605 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 222 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CD276 antigen222Mus musculusMutation(s): 0 
Gene Names: B7-H3B7h3Cd276
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VE98 (Mus musculus)
Explore Q8VE98 
Go to UniProtKB:  Q8VE98
IMPC:  MGI:2183926
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VE98
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q8VE98-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free:  0.250 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
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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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary