6R0X

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 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 10.7554/eLife.46840
  • Primary Citation of 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 ...

    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

    Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Grand Est, Unité Mixte de Recherche-S 1255, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
antibody fab fragment heavy chainA, C240Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
antibody fab fragment light chainB, D234Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Megakaryocyte and platelet inhibitory receptor G6bE, F116Homo 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranoseG, I3O-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56682BC
GlyCosmos:  G56682BC
GlyGen:  G56682BC
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseH8N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G40559JB
GlyCosmos:  G40559JB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • 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