6R0X | pdb_00006r0x

The extracellular domain of G6b-B in complex with Fab fragment and DP12 heparin oligosaccharide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 
    0.266 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6R0X

This is version 2.2 of the entry. See complete history

Literature

Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B.

Vogtle, T.Sharma, S.Mori, J.Nagy, Z.Semeniak, D.Scandola, C.Geer, M.J.Smith, C.W.Lane, J.Pollack, S.Lassila, R.Jouppila, A.Barr, A.J.Ogg, D.J.Howard, T.D.McMiken, H.J.Warwicker, J.Geh, C.Rowlinson, R.Abbott, W.M.Eckly, A.Schulze, H.Wright, G.J.Mazharian, A.Futterer, K.Rajesh, S.Douglas, M.R.Senis, Y.A.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.46840
  • Primary Citation Related Structures: 
    6R0X

  • PubMed Abstract: 

    The immunoreceptor tyrosine-based inhibition motif (ITIM)-containing receptor G6b-B is critical for platelet production and activation. Loss of G6b-B results in severe macrothrombocytopenia, myelofibrosis and aberrant platelet function in mice and humans. Using a combination of immunohistochemistry, affinity chromatography and proteomics, we identified the extracellular matrix heparan sulfate (HS) proteoglycan perlecan as a G6b-B binding partner. Subsequent in vitro biochemical studies and a cell-based genetic screen demonstrated that the interaction is specifically mediated by the HS chains of perlecan. Biophysical analysis revealed that heparin forms a high-affinity complex with G6b-B and mediates dimerization. Using platelets from humans and genetically modified mice, we demonstrate that binding of G6b-B to HS and multivalent heparin inhibits platelet and megakaryocyte function by inducing downstream signaling via the tyrosine phosphatases Shp1 and Shp2. Our findings provide novel insights into how G6b-B is regulated and contribute to our understanding of the interaction of megakaryocytes and platelets with glycans.


  • Organizational Affiliation
    • Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 131.71 kDa 
  • Atom Count: 7,896 
  • Modeled Residue Count: 1,047 
  • Deposited Residue Count: 1,180 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
antibody fab fragment heavy chain
A, C
240Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
antibody fab fragment light chain
B, D
234Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Megakaryocyte and platelet inhibitory receptor G6b
E, F
116Homo sapiensMutation(s): 5 
Gene Names: MPIG6BC6orf25G6BG6B-B
UniProt & NIH Common Fund Data Resources
Find proteins for O95866 (Homo sapiens)
Explore O95866 
Go to UniProtKB:  O95866
PHAROS:  O95866
GTEx:  ENSG00000204420 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95866
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O95866-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose
G, I
3O-Glycosylation
Glycosylation Resources
GlyTouCan: G56682BC
GlyCosmos: G56682BC
GlyGen: G56682BC
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
H
8N/A
Glycosylation Resources
GlyTouCan: G40559JB
GlyCosmos: G40559JB

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free:  0.266 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.8α = 90
b = 72.34β = 124.52
c = 131.042γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited KingdomRG/15/13/31673
British Heart FoundationUnited KingdomFS/13/1/29894

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary