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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RAT FGF1-SUCROSE OCTASULFATE (SOS) COMPLEX.
 
Authors :  N. Kulahin, V. Kiselyov, A. Kochoyan, O. Kristensen, V. Berezin, E. Bock, M. Gajhede
Date :  07 Mar 07  (Deposition) - 13 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Differentiation, Heparin-Binding, Sucrose Octasulfate, Developmental Protein, Fibroblast Growth Factor, Mitogen, Angiogenesis, Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kulahin, V. Kiselyov, A. Kochoyan, O. Kristensen, J. S. Kastrup, V. Berezin, E. Bock, M. Gajhede
Dimerization Effect Of Sucrose Octasulfate On Rat Fgf1.
Acta Crystallogr. , Sect. F V. 64 448 2008
PubMed-ID: 18540049  |  Reference-DOI: 10.1107/S174430910801066X

(-) Compounds

Molecule 1 - HEPARIN-BINDING GROWTH FACTOR 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP 10 F'
    Expression System Taxid: 562
    Expression System Vector: PQE-60
    Fragment: RESIDUES 22-153
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: HBGF-1, ACIDIC FIBROBLAST GROWTH FACTOR, AFGF, RAT FGF1, SUCROSE OCTASULFATE

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SCR1Ligand/IonSUCROSE OCTASULFATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SCR1Ligand/IonSUCROSE OCTASULFATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SCR-1Ligand/IonSUCROSE OCTASULFATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , LYS A:112 , LYS A:113 , LYS A:118 , ARG A:122 , HIS A:124 , GLN A:127 , LYS A:128 , HOH A:2081 , HOH A:2083 , HOH A:2087 , HOH A:2088 , HOH A:2089 , HOH A:2090 , HOH A:2091 , HOH A:2093 , HOH A:2094 , HOH A:2096 , HOH A:2097 , HOH A:2099 , HOH A:2100 , ASN B:18 , ASP B:28 , LYS B:113 , LYS B:118 , ARG B:122 , HIS B:124 , GLN B:127 , LYS B:128 , ALA B:129BINDING SITE FOR RESIDUE SCR A1138

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UUS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2UUS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UUS)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF1_RAT86-109
 		  2A:71-94
B:71-94
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF1_RAT86-109
 		  1A:71-94
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF1_RAT86-109
 		  1-
B:71-94

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000185771ENSRNOE00000132196chr18:31806452-31806220233FGF1_RAT-00--
1.2ENSRNOT000000185772ENSRNOE00000132294chr18:31801915-31801713203FGF1_RAT1-57572A:7-42
B:8-42		36
35
1.3ENSRNOT000000185773ENSRNOE00000132376chr18:31790940-31790837104FGF1_RAT57-91352A:42-76
B:42-76 (gaps)		35
35
1.4ENSRNOT000000185774ENSRNOE00000132447chr18:31786124-31785482643FGF1_RAT92-155642A:77-138
B:77-138		62
62

(-) 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:132
 aligned with FGF1_RAT | P61149 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:132
                                    31        41        51        61        71        81        91       101       111       121       131       141       151  
             FGF1_RAT    22 NYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESAGEVYIKGTETGQYLAMDTEGLLYGSQTPNEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVS 153
               SCOP domains d2uusa_ A: automated matches                                                                                                         SCOP domains
               CATH domains 2uusA00 A:7-138  [code=2.80.10.50, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....eeeee.....eeee....hhhh.eeeee....eeeeee.....eeee.....eeee...hhhh.eeeee.....eeeee..hhhhh............hhhhh...hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------HBGF_FGF  PDB: A:71-94  -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:7-42 UniProt: 1-57 ----------------------------------Exon 1.4  PDB: A:77-138 UniProt: 92-155 [INCOMPLETE]           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.3  PDB: A:42-76             -------------------------------------------------------------- Transcript 1 (2)
                 2uus A   7 NYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESAGEVYIKGTETGQYLAMDTEGLLYGSQTPNEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVS 138
                                    16        26        36        46        56        66        76        86        96       106       116       126       136  


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with FGF1_RAT | P61149 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:131
                                    32        42        52        62        72        82        92       102       112       122       132       142       152 
             FGF1_RAT    23 YKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESAGEVYIKGTETGQYLAMDTEGLLYGSQTPNEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVS 153
               SCOP domains d2uusb_ B: automated matches                                                                                                        SCOP domains
               CATH domains 2uusB00 B:8-138  [code=2.80.10.50, no name   defined]                                                                               CATH domains
           Pfam domains (1) --FGF-2uusB01 B:10-133                                                                                                        ----- Pfam domains (1)
           Pfam domains (2) --FGF-2uusB02 B:10-133                                                                                                        ----- Pfam domains (2)
         Sec.struct. author ....eeeee....eeeee.....eeee.........eeee..--.eeeeee.....eeee.....eeee...hhhh.eeeee.....eeeee..hhhhh............hhhhh...hhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------HBGF_FGF  PDB: B:71-94  -------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:8-42 UniProt: 1-57----------------------------------Exon 1.4  PDB: B:77-138 UniProt: 92-155 [INCOMPLETE]           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: B:42-76 (gaps)      -------------------------------------------------------------- Transcript 1 (2)
                 2uus B   8 YKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAE--GEVYIKGTETGQYLAMDTEGLLYGSQTPNEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPVS 138
                                    17        27        37        47 |  |   57        67        77        87        97       107       117       127       137 
                                                                    49 52
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Trefoil (131)
(-)
Family: FGF (36)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FGF1_RAT | P61149)
molecular function
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0032148    activation of protein kinase B activity    Any process that initiates the activity of the inactive enzyme protein kinase B.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0060681    branch elongation involved in ureteric bud branching    The growth of a branch of the ureteric bud along its axis.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0010595    positive regulation of endothelial cell migration    Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    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:1903672    positive regulation of sprouting angiogenesis    Any process that activates or increases the frequency, rate or extent of sprouting angiogenesis.
    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.
    GO:1901509    regulation of endothelial tube morphogenesis    Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis.
cellular component
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FGF1_RAT | P61149: 2j3p

(-) Related Entries Specified in the PDB File

2j3p CRYSTAL STRUCTURE OF RAT FGF1 AT 1.4 A