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 


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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
NEOGENINA264Homo sapiensMutation(s): 0 
Gene Names: NEO1IGDCC2NGN
UniProt & NIH Common Fund Data Resources
Find proteins for Q92859 (Homo sapiens)
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Go to UniProtKB:  Q92859
PHAROS:  Q92859
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BONE MORPHOGENETIC PROTEIN 2, BMP2B114Homo sapiensMutation(s): 0 
Gene Names: BMP2BMP2A
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Find proteins for P12643 (Homo sapiens)
Explore P12643 
Go to UniProtKB:  P12643
PHAROS:  P12643
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELINC122Homo sapiensMutation(s): 0 
Gene Names: RGMB
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Find proteins for Q6NW40 (Homo sapiens)
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Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIND251Homo sapiensMutation(s): 0 
Gene Names: RGMB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens)
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Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRT (Subject of Investigation/LOI)
Query on SRT

Download Ideal Coordinates CCD File 
F [auth B], G [auth B], H [auth B]S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
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  



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