8E3G

BMP2/GDF5 heterodimer

• PDB DOI: https://doi.org/10.2210/pdb8E3G/pdb

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


• Deposited: 2022-08-17 Released: 2023-02-15 
• Deposition Author(s): Gipson, G.R., Nolan, K.T., Thompson, T.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Formation and characterization of BMP2/GDF5 and BMP4/GDF5 heterodimers.

Gipson, G.R., Nolan, K., Kattamuri, C., Kenny, A.P., Agricola, Z., Edwards, N.A., Zinski, J., Czepnik, M., Mullins, M.C., Zorn, A.M., Thompson, T.B.

(2023) BMC Biol 21: 16-16

• PubMed: 36726183 
• DOI: https://doi.org/10.1186/s12915-023-01522-4
• Primary Citation of Related Structures:  
  8E3G


• PubMed Abstract: 
  

  Proteins of the TGFβ family, which are largely studied as homodimers, are also known to form heterodimers with biological activity distinct from their component homodimers. For instance, heterodimers of bone morphogenetic proteins, including BMP2/BMP7, BMP2/BMP6, and BMP9/BMP10, among others, have illustrated the importance of these heterodimeric proteins within the context of TGFβ signaling.

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Organizational Affiliation: 

Department of Molecular & Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 53.51 kDa 
• Atom Count: 3,326 
• Modelled Residue Count: 418 
• Deposited Residue Count: 468 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone morphogenetic protein 2	A, C	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth/differentiation factor 5	B, D	120	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth C], H [auth D], I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.321	α = 90
b = 98.321	β = 90
c = 174.783	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Gipson, G.R., Nolan, K.T., Thompson, T.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM134923-02

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 2.0: 2023-02-22
  Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Refinement description