2ERM | pdb_00002erm

Solution structure of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue

• PDB DOI: https://doi.org/10.2210/pdb2ERM/pdb

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-10-25 Released: 2006-10-03 
• Deposition Author(s): Canales, A., Lozano, R., Nieto, P.M., Martin-Lomas, M., Gimenez-Gallego, G., Jimenez-Barbero, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution NMR structure of a human FGF-1 monomer, activated by a hexasaccharide heparin-analogue.

Canales, A., Lozano, R., Lopez-Mendez, B., Angulo, J., Ojeda, R., Nieto, P.M., Martin-Lomas, M., Gimenez-Gallego, G., Jimenez-Barbero, J.

(2006) FEBS J 273: 4716-4727

• PubMed: 16995857 
• DOI: https://doi.org/10.1111/j.1742-4658.2006.05474.x
• Primary Citation Related Structures: 
  2ERM


• PubMed Abstract: 
  

  The 3D structure of a complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed synthetic heparin hexasaccharide has been determined by NMR spectroscopy. This hexasaccharide can substitute natural heparins in FGF-1 mitogenesis assays, in spite of not inducing any apparent dimerization of the growth factor. The use of this well defined synthetic heparin analogue has allowed us to perform a detailed NMR structural analysis of the heparin-FGF interaction, overcoming the limitations of NMR to deal with the high molecular mass and heterogeneity of the FGF-1 oligomers formed in the presence of natural heparin fragments. Our results confirm that glycosaminoglycans induced FGF-1 dimerization either in a cis or trans disposition with respect to the heparin chain is not an absolute requirement for biological activity.

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Organizational Affiliation: 
• Centro de Investigaciones Biológicas,CSIC, Madrid, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.24 kDa 
• Atom Count: 1,160 
• Modeled Residue Count: 133 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparin-binding growth factor 1	A	139	Homo sapiens	Mutation(s): 0  Gene Names: FGF1, FGFA
UniProt & NIH Common Fund Data Resources
Find proteins for P05230 (Homo sapiens) Explore P05230  Go to UniProtKB:  P05230
PHAROS:  P05230 GTEx:  ENSG00000113578

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid	B	6		N/A
Glycosylation Resources
GlyTouCan: G09918ME GlyCosmos: G09918ME

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	C [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Canales, A., Lozano, R., Nieto, P.M., Martin-Lomas, M., Gimenez-Gallego, G., Jimenez-Barbero, J.

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  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: 2024-05-01
  Changes: Data collection, Database references, Structure summary