4BQ8

Crystal structure of the RGMB-NEO1 complex form 3


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • 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) ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEOGENIN A213Mus musculusMutation(s): 0 
Gene Names: Neo1Ngn
Find proteins for P97798 (Mus musculus)
Explore P97798 
Go to UniProtKB:  P97798
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RGM DOMAIN FAMILY MEMBER B B122Homo sapiensMutation(s): 0 
Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens)
Explore Q6NW40 
Go to UniProtKB:  Q6NW40
NIH Common Fund Data Resources
PHAROS:  Q6NW40
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RGM DOMAIN FAMILY MEMBER B C251Homo sapiensMutation(s): 0 
Gene Names: RGMB
Find proteins for Q6NW40 (Homo sapiens)
Explore Q6NW40 
Go to UniProtKB:  Q6NW40
NIH Common Fund Data Resources
PHAROS:  Q6NW40
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
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 = 116.92α = 90
b = 116.92β = 90
c = 91.82γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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