4BQ8 | pdb_00004bq8

Crystal structure of the RGMB-NEO1 complex form 3

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.199 (Depositor), 0.209 (DCC)
R-Value Work:
0.183 (Depositor), 0.188 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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

PubMed: 23744777 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1232322
Primary Citation Related Structures:
4BQ6, 4BQ7, 4BQ8, 4BQ9, 4BQB, 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 65.56 kDa
Atom Count: 2,924
Modeled Residue Count: 370
Deposited Residue Count: 586
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEOGENIN	A	213	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P97798 (Mus musculus) Explore P97798 Go to UniProtKB: P97798
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P97798
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P97798-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RGM DOMAIN FAMILY MEMBER B	B	122	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens) Explore Q6NW40 Go to UniProtKB: Q6NW40
PHAROS: Q6NW40 GTEx: ENSG00000174136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NW40
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RGM DOMAIN FAMILY MEMBER B	C	251	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NW40 (Homo sapiens) Explore Q6NW40 Go to UniProtKB: Q6NW40
PHAROS: Q6NW40 GTEx: ENSG00000174136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NW40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.199 (Depositor), 0.209 (DCC)
R-Value Work: 0.183 (Depositor), 0.188 (DCC)
R-Value Observed: 0.184 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

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
Version 1.5: 2024-11-20
Changes: Data collection, Database references, Structure summary