Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 65.56 kDa 
• Atom Count: 2924 
• Modelled Residue Count: 370 
• Deposited Residue Count: 586 
• Unique protein chains: 3

4BQ8

Crystal structure of the RGMB-NEO1 complex form 3

• DOI: 10.2210/pdb4BQ8/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2013-06-12 
• Deposition Author(s): Bell, C.H., Healey, E., van Erp, S., Bishop, B., Tang, C., Gilbert, R.J.C., Aricescu, A.R., Pasterkamp, R.J., Siebold, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Structure of the Repulsive Guidance Molecule (Rgm)-Neogenin Signaling Hub

Bell, C.H., Healey, E., Van Erp, S., Bishop, B., Tang, C., Gilbert, R.J.C., Aricescu, A.R., Pasterkamp, R.J., Siebold, C.

(2013) Science 341: 77

• PubMed: 23744777 
• DOI: 10.1126/science.1232322
• Primary Citation of Related Structures:  
  4BQB, 4BQ6, 4BQ7, 4BQ8, 4BQ9, 4BQC


• PubMed Abstract: 
  

Repulsive guidance molecule family members (RGMs) control fundamental and diverse cellular processes, including motility and adhesion, immune cell regulation, and systemic iron metabolism. However, it is not known how RGMs initiate signaling through their common cell-surface receptor, neogenin (NEO1). Here, we present crystal structures of the NEO1 RGM-binding region and its complex with human RGMB (also called dragon). The RGMB structure reveals a previously unknown protein fold and a functionally important autocatalytic cleavage mechanism and provides a framework to explain numerous disease-linked mutations in RGMs. In the complex, two RGMB ectodomains conformationally stabilize the juxtamembrane regions of two NEO1 receptors in a pH-dependent manner. We demonstrate that all RGM-NEO1 complexes share this architecture, which therefore represents the core of multiple signaling pathways.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEOGENIN	A	213	Mus musculus	Mutation(s): 0  Gene Names: Neo1, Ngn
Find proteins for P97798 (Mus musculus) Explore P97798  Go to UniProtKB:  P97798

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RGM DOMAIN FAMILY MEMBER B	B	122	Homo sapiens	Mutation(s): 0  Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens) Explore Q6NW40  Go to UniProtKB:  Q6NW40
NIH Common Fund Data Resources
PHAROS:  Q6NW40 GTEx:  ENSG00000174136

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RGM DOMAIN FAMILY MEMBER B	C	251	Homo sapiens	Mutation(s): 0  Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens) Explore Q6NW40  Go to UniProtKB:  Q6NW40
NIH Common Fund Data Resources
PHAROS:  Q6NW40 GTEx:  ENSG00000174136

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.92	α = 90
b = 116.92	β = 90
c = 91.82	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-30 
• Released Date: 2013-06-12 
Deposition Author(s): Bell, C.H., Healey, E., van Erp, S., Bishop, B., Tang, C., Gilbert, R.J.C., Aricescu, A.R., Pasterkamp, R.J., Siebold, C.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2013-07-17
  Changes: Database references
• Version 1.3: 2019-04-03
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary