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(-) Description

Title :  CRYSTAL STRUCTURE OF RABBIT ACIDIC FIBROBLAST GROWTH FACTOR
 
Authors :  M. Blaber, J. Lee
Date :  01 May 09  (Deposition) - 22 Dec 09  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Trefoil, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lee, S. I. Blaber, A. Irsigler, E. Aspinwall, M. Blaber
X-Ray Structure And Biophysical Properties Of Rabbit Fibroblast Growth Factor 1.
Acta Crystallogr. , Sect. F V. 65 1097 2009
PubMed-ID: 19923726  |  Reference-DOI: 10.1107/S1744309109040287
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR 1 ISOFORM 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFGF1
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , LYS A:112 , LYS A:113 , LYS A:118 , HOH A:241BINDING SITE FOR RESIDUE SO4 A 141
2AC2SOFTWAREARG A:119BINDING SITE FOR RESIDUE CL A 142
3AC3SOFTWAREASN B:18 , LYS B:112 , LYS B:113 , LYS B:118 , HOH B:250BINDING SITE FOR RESIDUE SO4 B 141
4AC4SOFTWARELYS B:112 , ARG B:119BINDING SITE FOR RESIDUE CL B 142

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HAL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HAL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HAL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HAL)

(-) Exons   (0, 0)

(no "Exon" information available for 3HAL)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:131
 aligned with B7NZB1_RABIT | B7NZB1 from UniProtKB/TrEMBL  Length:155

    Alignment length:131
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 
         B7NZB1_RABIT    22 NYKLPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV 152
               SCOP domains d3hala_ A: Acidic FGF (FGF1)                                                                                                        SCOP domains
               CATH domains 3halA00 A:7-137  [code=2.80.10.50, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeee.....eeee.........eeeee....eeeeee.....eeee.....eeee...hhhh.eeeee.hhh.eeeee..hhhhh............hhhhh...hhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hal A   7 NYKLPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV 137
                                    16        26        36        46        56        66        76        86        96       106       116       126       136 

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with B7NZB1_RABIT | B7NZB1 from UniProtKB/TrEMBL  Length:155

    Alignment length:131
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 
         B7NZB1_RABIT    22 NYKLPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV 152
               SCOP domains d3halb_ B: Acidic FGF (FGF1)                                                                                                        SCOP domains
               CATH domains 3halB00 B:7-137  [code=2.80.10.50, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeee.....eeee.........eeeee....eeeeee.....eeee.....eeee...hhhh.eeeee.hhh.eeeee..hhhhh............hhhhh...hhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hal B   7 NYKLPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTDGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV 137
                                    16        26        36        46        56        66        76        86        96       106       116       126       136 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HAL)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (B7NZB1_RABIT | B7NZB1)
molecular function
    GO:0044548    S100 protein binding    Interacting selectively and non-covalently with a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS.
    GO:0005104    fibroblast growth factor receptor binding    Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR).
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0060681    branch elongation involved in ureteric bud branching    The growth of a branch of the ureteric bud along its axis.
    GO:0034605    cellular response to heat    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0072163    mesonephric epithelium development    The process whose specific outcome is the progression of an epithelium in the mesonephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
    GO:0001759    organ induction    The interaction of two or more cells or tissues that causes them to change their fates and specify the development of an organ.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045542    positive regulation of cholesterol biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cholesterol.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:1902533    positive regulation of intracellular signal transduction    Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:2000544    regulation of endothelial cell chemotaxis to fibroblast growth factor    Any process that modulates the frequency, rate or extent of endothelial cell chemotaxis to fibroblast growth factor.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1jqz HUMAN ACIDIC FIBROBLAST GROWTH FACTOR. 141 AMINO ACID FORM WITH AMINO TERMINAL HIS TAG