4UHZ

Crystal structure of the human RGMB-BMP2 complex, crystal form 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BONE MORPHOGENETIC PROTEIN 2114Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12643
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RGM DOMAIN FAMILY MEMBER B96Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens)
Explore Q6NW40 
Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
GTEx:  ENSG00000174136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NW40
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.01α = 90
b = 129.01β = 90
c = 129.01γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary