Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84541.63 
• Atom Count: 4311 
• Residue Count: 751 
• Unique protein chains: 4

4UI2

Crystal structure of the ternary RGMB-BMP2-NEO1 complex

• DOI: 10.2210/pdb4UI2/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)


• Deposited: 2015-03-27 Released: 2015-05-06 
• Deposition Author(s): Healey, E.G., Bishop, B., Elegheert, J., Bell, C.H., Padilla-Parra, S., Siebold, C.

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Experimental Data Snapshot

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

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

• PubMed: 25938661 
• DOI: 10.1038/nsmb.3016
• Primary Citation of Related Structures:  
  4UI1, 4UI0, 4UHZ, 4UHY


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
NEOGENIN	A	264	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
BONE MORPHOGENETIC PROTEIN 2, BMP2	B	114	Homo sapiens	Mutation(s): 0  Gene Names: BMP2 (BMP2A)
Find proteins for P12643 (Homo sapiens) Go to Gene View: BMP2 Go to UniProtKB:  P12643

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN	C	122	Homo sapiens	Mutation(s): 0  Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens) Go to Gene View: RGMB Go to UniProtKB:  Q6NW40

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN	D	251	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ACT	B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
SRT	B	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 120.080	α = 90.00
b = 120.080	β = 90.00
c = 204.090	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-27 
• Released Date: 2015-05-06 
• Deposition Author(s): Healey, E.G., Bishop, B., Elegheert, J., Bell, C.H., Padilla-Parra, S., Siebold, C.

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