PDBsum entry: 1rg8

Hormone/growth factor

PDB id: 1rg8

Contents

Protein chains

141 a.a. *

Ligands

FMT ×5

Waters ×403

* Residue conservation analysis

PDB id:

1rg8

Name:

Hormone/growth factor

Title:

Human acidic fibroblast growth factor (hafgf-1) at 1.10 angstrom resolution (140 amino acid form)

Structure:

Heparin-binding growth factor 1. Chain: a, b. Synonym: hbgf-1, acidic fibroblast growth factor, afgf, beta-endothelial cell growth factor, ecgf-beta. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: fgf1, fgfa. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.10Å R-factor: 0.147 R-free: 0.171

Authors:

M.J.Bernett,T.Somasundaram,M.Blaber

Key ref:

M.J.Bernett et al. (2004). An atomic resolution structure for human fibroblast growth factor 1. Proteins, 57, 626-634. PubMed id: 15382229 DOI: 10.1002/prot.20239

Date:

11-Nov-03 Release date: 05-Oct-04

Protein chains

P05230  (FGF1_HUMAN) -  Heparin-binding growth factor 1

Seq: 155 a.a.

Struc: 141 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (8 terms)
• Biological process: multicellular organismal development (22 terms)
• Biochemical function: protein binding (6 terms)

DOI no: 10.1002/prot.20239

Proteins 57:626-634 (2004)

PubMed id: 15382229

An atomic resolution structure for human fibroblast growth factor 1.

M.J.Bernett, T.Somasundaram, M.Blaber.

ABSTRACT

A 1.10-A atomic resolution X-ray structure of human fibroblast growth factor 1 (FGF-1), a member of the beta-trefoil superfold, has been determined. The beta-trefoil is one of 10 fundamental protein superfolds and is the only superfold to exhibit 3-fold structural symmetry (comprising 3 "trefoil" units). The quality of the diffraction data permits unambiguous assignment of Asn, Gln, and His rotamers, Pro ring pucker, as well as refinement of atomic anisotropic displacement parameters (ADPs). The FGF-1 structure exhibits numerous core-packing defects, detectable using a 1.0-A probe radius. In addition to contributing to the relatively low thermal stability of FGF-1, these defects may also permit domain motions within the structure. The availability of refined ADPs allows a translation/libration/screw (TLS) analysis of putative rigid body domains. The TLS analysis shows that beta-strands 6-12 together form a rigid body, and there is a clear demarcation in TLS motions between the adjacent carboxyl- and amino-termini. Although separate from beta-strands 6-12, the individual beta-strands 1-5 do not exhibit correlated motions; thus, this region appears to be comparatively flexible. The heparin-binding contacts of FGF-1 are located within beta-strands 6-12; conversely, a significant portion of the receptor-binding contacts are located within beta-strands 1-5. Thus, the observed rigid body motion in FGF-1 appears related to the ligand-binding functionalities.

Selected figure(s)

Figure 1.
Figure 1. Top panel: A schematic representation of the secondary structure of FGF-1, and the numbering of the individual -strands. The -strands comprising the trefoil subdomains 1-3 are indicated by the black, gray, and white shading, respectively. The amino and carboxyl termini are indicated. Middle panel: A relaxed stereo ribbon diagram of FGF-1 as a side view. Bottom panel: A relaxed stereo diagram looking down the 3-fold axis of structural symmetry.

Figure 6.
Figure 6. FGF/FGFR/heparin ternary complex.[45] FGF is shown in space-filling representation with the rigid body domain comprising -strands 1-5 indicated in red, and the domain comprising -strands 6-12 in blue. The heparin polysaccharide component of the complex is shown in green space-filling representation. The two Ig-like ligand-binding domains of the FGFR are rendered in a ribbon representation. The upper panel shows the ternary complex, while the lower panel shows a single FGF/FGFR complex to highlight the interaction of -strands 1-5, with the two Ig-like domains in a single receptor molecule. The lower panel is rotated approximately 90° about the vertical axis in relationship to the upper panel.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 626-634) copyright 2004.

Figures were selected by the author.