5JHW

Crystal Structure of the GDF11:Follistatin 288 complex

PDB DOI: https://doi.org/10.2210/pdb5JHW/pdb

Classification: CYTOKINE/Signaling Protein
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2016-04-21 Released: 2017-03-22
Deposition Author(s): Walker, R.G., Thompson, T.B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Muscular Dystrophy Association, American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.247
R-Value Work: 0.202
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for potency differences between GDF8 and GDF11.

Walker, R.G., Czepnik, M., Goebel, E.J., McCoy, J.C., Vujic, A., Cho, M., Oh, J., Aykul, S., Walton, K.L., Schang, G., Bernard, D.J., Hinck, A.P., Harrison, C.A., Martinez-Hackert, E., Wagers, A.J., Lee, R.T., Thompson, T.B.

(2017) BMC Biol 15: 19-19

PubMed: 28257634 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12915-017-0350-1
Primary Citation of Related Structures:
5JHW, 5JI1, 5UHM

PubMed Abstract:
Growth/differentiation factor 8 (GDF8) and GDF11 are two highly similar members of the transforming growth factor β (TGFβ) family. While GDF8 has been recognized as a negative regulator of muscle growth and differentiation, there are conflicting studies on the function of GDF11 and whether GDF11 has beneficial effects on age-related dysfunction. To address whether GDF8 and GDF11 are functionally identical, we compared their signaling and structural properties.

Organizational Affiliation

Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH, 45267, USA.

Macromolecule Content

Total Structure Weight: 89.74 kDa
Atom Count: 6,323
Modelled Residue Count: 784
Deposited Residue Count: 794
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth/differentiation factor 11	A, B	109	Homo sapiens	Mutation(s): 0 Gene Names: GDF11, BMP11
UniProt & NIH Common Fund Data Resources
Find proteins for O95390 (Homo sapiens) Explore O95390 Go to UniProtKB: O95390
PHAROS: O95390 GTEx: ENSG00000135414
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95390
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Follistatin	C, D	288	Homo sapiens	Mutation(s): 0 Gene Names: FST
UniProt & NIH Common Fund Data Resources
Find proteins for P19883 (Homo sapiens) Explore P19883 Go to UniProtKB: P19883
PHAROS: P19883 GTEx: ENSG00000134363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D]	F [auth A] G [auth B] H [auth B] J [auth C] K [auth C] F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], L [auth D], M [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain N [auth D]	E [auth A], I [auth C], N [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.247
R-Value Work: 0.202
R-Value Observed: 0.205
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.96	α = 90
b = 59.08	β = 90
c = 288.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Walker, R.G.

Thompson, T.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM114640
Muscular Dystrophy Association	United States	240087
American Heart Association	United States	12PRE11790027

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description