4UI2

Crystal structure of the ternary RGMB-BMP2-NEO1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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This is version 2.0 of the entry. See complete history


Literature

Repulsive Guidance Molecule is a Structural Bridge between Neogenin and Bone Morphogenetic Protein.

Healey, E.G.Bishop, B.Elegheert, J.Bell, C.H.Padilla-Parra, S.Siebold, C.

(2015) Nat Struct Mol Biol 22: 458

  • DOI: https://doi.org/10.1038/nsmb.3016
  • Primary Citation of Related Structures:  
    4UHY, 4UHZ, 4UI0, 4UI1, 4UI2

  • PubMed Abstract: 

    Repulsive guidance molecules (RGMs) control crucial processes including cell motility, adhesion, immune-cell regulation and systemic iron metabolism. RGMs signal via the neogenin (NEO1) and the bone morphogenetic protein (BMP) pathways. Here, we report crystal structures of the N-terminal domains of all human RGM family members in complex with the BMP ligand BMP2, revealing a new protein fold and a conserved BMP-binding mode. Our structural and functional data suggest a pH-linked mechanism for RGM-activated BMP signaling and offer a rationale for RGM mutations causing juvenile hemochromatosis. We also determined the crystal structure of the ternary BMP2-RGM-NEO1 complex, which, along with solution scattering and live-cell super-resolution fluorescence microscopy, indicates BMP-induced clustering of the RGM-NEO1 complex. Our results show how RGM acts as the central hub that links BMP and NEO1 and physically connects these fundamental signaling pathways.


  • Organizational Affiliation

    1] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Cellular Imaging Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEOGENIN264Homo sapiensMutation(s): 0 
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Find proteins for Q92859 (Homo sapiens)
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Go to UniProtKB:  Q92859
GTEx:  ENSG00000067141 
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UniProt GroupQ92859
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BONE MORPHOGENETIC PROTEIN 2, BMP2114Homo sapiensMutation(s): 0 
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Go to UniProtKB:  P12643
GTEx:  ENSG00000125845 
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UniProt GroupP12643
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN122Homo sapiensMutation(s): 0 
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Go to UniProtKB:  Q6NW40
GTEx:  ENSG00000174136 
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UniProt GroupQ6NW40
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN251Homo sapiensMutation(s): 0 
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Find proteins for Q6NW40 (Homo sapiens)
Explore Q6NW40 
Go to UniProtKB:  Q6NW40
GTEx:  ENSG00000174136 
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UniProt GroupQ6NW40
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.08α = 90
b = 120.08β = 90
c = 204.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-06-17
    Changes: Database references
  • Version 1.3: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary