6Z3M

Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1).

• PDB DOI: https://doi.org/10.2210/pdb6Z3M/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-05-21 Released: 2020-07-01 
• Deposition Author(s): Malinauskas, T., Peer, T.V., Bishop, B., Muller, T.D., Siebold, C.
• Funding Organization(s): Cancer Research UK, European Research Council (ERC), German Research Foundation (DFG), Wellcome Trust, Human Frontier Science Program (HFSP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free: 0.428 
• R-Value Work: 0.326 
• R-Value Observed: 0.331 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 989.27 kDa 
• Atom Count: 25,210 
• Modelled Residue Count: 3,257 
• Deposited Residue Count: 8,898 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth/differentiation factor 5	A, B, G, H, M, N	117	Homo sapiens	Mutation(s): 0  Gene Names: GDF5, BMP14, CDMP1
UniProt & NIH Common Fund Data Resources
Find proteins for P43026 (Homo sapiens) Explore P43026  Go to UniProtKB:  P43026
PHAROS:  P43026 GTEx:  ENSG00000125965

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RGM domain family member B	AA [auth U], BA [auth V], C, CA [auth W], D, DA [auth X], I, J, O, P, S [auth c], T [auth d], U [auth i], V [auth j], W [auth o], X [auth p], Y [auth S], Z [auth T]	371	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Neogenin	E, F, K, L, Q, R	253	Mus musculus	Mutation(s): 0  Gene Names: Neo1, Ngn
UniProt
Find proteins for P97798 (Mus musculus) Explore P97798  Go to UniProtKB:  P97798

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	EA [auth D], FA [auth E], GA [auth F], HA [auth I], IA [auth K], JA [auth L], KA [auth P], LA [auth Q], MA [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free: 0.428 
• R-Value Work: 0.326 
• R-Value Observed: 0.331 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 279.48	α = 90
b = 279.48	β = 90
c = 142.37	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Malinauskas, T., Peer, T.V., Bishop, B., Muller, T.D., Siebold, C.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C20724/A14414
Cancer Research UK	United Kingdom	C20724/A26752
European Research Council (ERC)	European Union	647278
German Research Foundation (DFG)	Germany	MU1095/3-2
German Research Foundation (DFG)	Germany	MU1095/5-1
Wellcome Trust	United Kingdom	203852/Z/16/2
Human Frontier Science Program (HFSP)	France	LT000021/2014-L

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2020-07-15
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-05-24
  Changes: Database references, Structure summary
• Version 1.5: 2023-07-26
  Changes: Author supporting evidence, Other
• Version 1.6: 2024-02-07
  Changes: Data collection, Refinement description