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 

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: 10.1038/nsmb.3016
  • Primary Citation of Related Structures:  

  • 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 repo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEOGENIN
A
264Homo sapiensMutation(s): 0 
Gene Names: NEO1 (IGDCC2, NGN)
Find proteins for Q92859 (Homo sapiens)
Go to Gene View: NEO1
Go to UniProtKB:  Q92859
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BONE MORPHOGENETIC PROTEIN 2, BMP2
B
114Homo sapiensMutation(s): 0 
Gene Names: BMP2 (BMP2A)
Find proteins for P12643 (Homo sapiens)
Go to Gene View: BMP2
Go to UniProtKB:  P12643
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
C
122Homo sapiensMutation(s): 0 
Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens)
Go to Gene View: RGMB
Go to UniProtKB:  Q6NW40
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN
D
251Homo sapiensMutation(s): 0 
Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens)
Go to Gene View: RGMB
Go to UniProtKB:  Q6NW40
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
SRT
Query on SRT

Download SDF File 
Download CCD File 
B
S,R MESO-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-XIXRPRMCSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 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 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.080α = 90.00
b = 120.080β = 90.00
c = 204.090γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-20
    Type: Database references
  • Version 1.2: 2015-06-17
    Type: Database references
  • Version 1.3: 2018-06-20
    Type: Advisory, Data collection, Derived calculations