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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN PLACENTA GROWTH FACTOR-1 (PLGF-1), AN ANGIOGENIC PROTEIN AT 2.0A RESOLUTION
 
Authors :  S. Iyer, D. D. Leonidas, G. J. Swaminathan, D. Maglione, M. Battisti, M. Tucci, M. G. Persico, K. R. Acharya
Date :  04 Oct 00  (Deposition) - 09 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine-Knot Family, Growth Factor, Angiogenesis, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Iyer, D. D. Leonidas, G. J. Swaminathan, D. Maglione, M. Battisti, M. Tucci, M. G. Persico, K. R. Acharya
The Crystal Structure Of Human Placenta Growth Factor-1 (Plgf-1), An Angiogenic Protein, At 2. 0 A Resolution.
J. Biol. Chem. V. 276 12153 2001
PubMed-ID: 11069911  |  Reference-DOI: 10.1074/JBC.M008055200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLACENTA GROWTH FACTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLGF-1
    TissuePLACENTA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:47 , TYR A:48 , TYR A:100 , THR A:104 , PHE A:105 , HOH A:203BINDING SITE FOR RESIDUE MPD A 201
2AC2SOFTWAREGLU B:47 , TYR B:100 , THR B:104 , PHE B:105 , HOH B:203BINDING SITE FOR RESIDUE MPD B 202

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:77
2A:60 -B:69
3A:66 -A:111
4A:69 -B:60
5A:70 -A:113
6B:35 -B:77
7B:66 -B:111
8B:70 -B:113

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:57 -Pro A:58
2Ser B:57 -Pro B:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FZV)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.PLGF_HUMAN39-131
 
  2A:22-114
B:22-114
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.PLGF_HUMAN75-87
 
  2A:58-70
B:58-70

(-) Exons   (0, 0)

(no "Exon" information available for 1FZV)

(-) Sequences/Alignments

Asymmetric/Biological 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:100
 aligned with PLGF_HUMAN | P49763 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:172
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  
           PLGF_HUMAN    35 SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRHSPGRQSPDMPGDFRADAPSFLPPRRSLPMLFRMEWGCALTGSQSAVWPSSPVPEEIPRMHPGRNGKKQQRKPLR 206
               SCOP domains d1fzva_ A: Placenta growth factor-1, PLGF-1                                                                                                                                  SCOP domains
               CATH domains 1fzvA00 A:18-117 Cystine-knot cytokines                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhhh.eeeeeeee.hhhh.......ee..eeeeeeee.......eeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee------------------------------------------------------------------------e.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PDGF_2  PDB: A:22-114 UniProt: 39-131                                                        --------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------PDGF_1       ----------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fzv A  18 SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECR------------------------------------------------------------------------PLR 117
                                    27        37        47        57        67        77        87        97       107      |  -         -         -         -         -         -         -       115  
                                                                                                                          114                                                                      115  

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with PLGF_HUMAN | P49763 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:172
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  
           PLGF_HUMAN    35 SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRHSPGRQSPDMPGDFRADAPSFLPPRRSLPMLFRMEWGCALTGSQSAVWPSSPVPEEIPRMHPGRNGKKQQRKPLR 206
               SCOP domains d1fzvb_ B: Placenta growth factor-1, PLGF-1                                                                                                                                  SCOP domains
               CATH domains 1fzvB00 B:18-117 Cystine-knot cytokines                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eehhhhhhhhhh.eeeeeeee.hhhh.......ee..eeeeeeee.......eeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee------------------------------------------------------------------------e.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PDGF_2  PDB: B:22-114 UniProt: 39-131                                                        --------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------PDGF_1       ----------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fzv B  18 SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECR------------------------------------------------------------------------PLR 117
                                    27        37        47        57        67        77        87        97       107      |  -         -         -         -         -         -         -       115  
                                                                                                                          114                                                                      115  

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FZV)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PLGF_HUMAN | P49763)
molecular function
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0001658    branching involved in ureteric bud morphogenesis    The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
    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:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0032870    cellular response to hormone stimulus    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 hormone stimulus.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    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: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:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0060688    regulation of morphogenesis of a branching structure    Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002040    sprouting angiogenesis    The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLGF_HUMAN | P497631rv6

(-) Related Entries Specified in the PDB File

1flt 1FLT CONTAINS VEGF IN COMPLEX WITH FLT-1, A RECEPTOR FOR PLGF AS WELL
2vpf 2VPF BELONGS TO THE SAME FAMILY OF CYSTEINE-KNOT GROWTH FACTORS AS PLGF