1G82

STRUCTURE OF FIBROBLAST GROWTH FACTOR 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.248 (Depositor) 
  • R-Value Work: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 3.0 of the entry. See complete history


Literature

Structure of fibroblast growth factor 9 shows a symmetric dimer with unique receptor- and heparin-binding interfaces.

Hecht, H.J.Adar, R.Hofmann, B.Bogin, O.Weich, H.Yayon, A.

(2001) Acta Crystallogr D Biol Crystallogr 57: 378-384

  • DOI: https://doi.org/10.1107/s0907444900020813
  • Primary Citation of Related Structures:  
    1G82

  • PubMed Abstract: 

    Fibroblast growth factors (FGFs) constitute a family of at least 20 structurally related heparin-binding polypeptides active in regulating cell growth, survival, differentiation and migration. FGF9, originally discovered as a glia-activating factor, shares 30% sequence identity with other FGFs and has a unique spectrum of target-cell specificity. FGF9 crystallized in the tetragonal space group I4(1), with unit-cell parameters a = b = 151.9, c = 117.2 A. The structure of the glycosylated protein has been refined to an R value of 21.0% with R(free) = 24.8%) at 2.6 A resolution. The four molecules in the asymmetric unit are arranged in two non-crystallographic dimers, with the dimer interface composed partly of residues from N- and C-terminal extensions from the FGF core structure. Most of the receptor-binding residues identified in FGF1- and FGF2-receptor complexes are buried in the dimer interface, with the beta8-beta9 loop stabilized in a particular conformation by an intramolecular hydrogen-bonding network. The potential heparin-binding sites are in a pattern distinct from FGF1 and FGF2. The carbohydrate moiety attached at Asn79 has no structural influence.


  • Organizational Affiliation

    Department SF, GBF - Gesellschaft für Biotechnologische Forschung, Mascheroder Weg 1, D-38124 Braunschweig, Germany. hjh@gbf.de


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FIBROBLAST GROWTH FACTOR 9
A, B, C, D
160Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P31371 (Homo sapiens)
Explore P31371 
Go to UniProtKB:  P31371
PHAROS:  P31371
GTEx:  ENSG00000102678 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31371
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P31371-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
L [auth B]
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.248 (Depositor) 
  • R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.947α = 90
b = 151.947β = 90
c = 117.23γ = 90
Software Package:
Software NamePurpose
EPMRphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-09
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary