RCSB PDB - 4UI2: Crystal structure of the ternary RGMB-BMP2-NEO1 complex

 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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Ligand Structure Quality Assessment 

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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

    Division of Structural Biology, 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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92859 (Homo sapiens)
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Go to UniProtKB:  Q92859
PHAROS:  Q92859
GTEx:  ENSG00000067141 
Entity Groups  
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UniProt GroupQ92859
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q92859-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BONE MORPHOGENETIC PROTEIN 2, BMP2114Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P12643 (Homo sapiens)
Explore P12643 
Go to UniProtKB:  P12643
PHAROS:  P12643
GTEx:  ENSG00000125845 
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UniProt GroupP12643
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN122Homo sapiensMutation(s): 0 
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Find proteins for Q6NW40 (Homo sapiens)
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Go to UniProtKB:  Q6NW40
PHAROS:  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
PHAROS:  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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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SRTClick on this verticalbar to view details

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