Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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: 84.51 kDa 
• Atom Count: 4311 
• Modelled Residue Count: 541 
• Deposited 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)
• Mutation(s): No 


• 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 
• R-Value Observed: 0.198 

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:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEOGENIN	A	264	Homo sapiens	Mutation(s): 0  Gene Names: NEO1, IGDCC2, NGN
UniProt & NIH Common Fund Data Resources
Find proteins for Q92859 (Homo sapiens) Explore Q92859  Go to UniProtKB:  Q92859
PHAROS:  Q92859 GTEx:  ENSG00000067141

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BONE MORPHOGENETIC PROTEIN 2, BMP2	B	114	Homo sapiens	Mutation(s): 0  Gene Names: BMP2, BMP2A
UniProt & NIH Common Fund Data Resources
Find proteins for P12643 (Homo sapiens) Explore P12643  Go to UniProtKB:  P12643
PHAROS:  P12643 GTEx:  ENSG00000125845

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN	C	122	Homo sapiens	Mutation(s): 0  Gene Names: RGMB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens) Explore Q6NW40  Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40 GTEx:  ENSG00000174136

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN	D	251	Homo sapiens	Mutation(s): 0  Gene Names: RGMB
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens) Explore Q6NW40  Go to UniProtKB:  Q6NW40
PHAROS:  Q6NW40 GTEx:  ENSG00000174136

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRT (Subject of Investigation/LOI)	F [auth B], G [auth B], H [auth B]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
ACT	I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 = 120.08	α = 90
b = 120.08	β = 90
c = 204.09	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  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