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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR-B: IDENTIFICATION OF AMINO ACIDS IMPORTANT FOR ANGIOGENINC ACTIVITY
 
Authors :  S. Iyer, P. D. Scotney, A. D. Nash, K. R. Acharya
Date :  29 Nov 05  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vascular Endothelial Growth Factor-B, Angiogenesis, Cysteine-Knot Motif, Tyrosine Kinase, Ischemia, Mitogen, Glycoprotein, Growth Factor, Heparin-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Iyer, P. D. Scotney, A. D. Nash, K. R. Acharya
Crystal Structure Of Human Vascular Endothelial Growth Factor-B: Identification Of Amino Acids Important For Receptor Binding
J. Mol. Biol. V. 359 76 2006
PubMed-ID: 16616187  |  Reference-DOI: 10.1016/J.JMB.2006.03.002

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR B PRECURSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VASCULAR ENDOTHELIAL GROWTH FACTOR-B, VEGF-B, VEGF RELATED FACTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:79 , LEU A:90 , GLY A:91 , GLU A:92 , GLN B:79 , LEU B:90 , GLU B:92BINDING SITE FOR RESIDUE MPD B1108

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:68
2A:51 -B:60
3A:57 -A:101
4A:60 -B:51
5A:61 -A:103
6B:26 -B:68
7B:57 -B:101
8B:61 -B:103

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:48 -Pro A:49
2Val B:48 -Pro B:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C7W)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.VEGFB_HUMAN34-129
 		  2A:13-108
B:13-108
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.VEGFB_HUMAN70-82
 		  2A:49-61
B:49-61

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003094221ENSE00001238390chr11:64002266-64002365100VEGFB_HUMAN1-20200--
1.2ENST000003094222ENSE00001238372chr11:64002930-6400297243VEGFB_HUMAN21-35152A:13-14
B:13-14		2
2
1.3ENST000003094223ENSE00001195939chr11:64003285-64003481197VEGFB_HUMAN35-100662A:14-79
B:14-79		66
66
1.4ENST000003094224ENSE00001195931chr11:64003726-6400379974VEGFB_HUMAN101-125252A:80-104
B:80-104		25
25
1.5ENST000003094225ENSE00001195925chr11:64004659-6400469436VEGFB_HUMAN125-137132A:104-108
B:104-108		5
5
1.6aENST000003094226aENSE00001238383chr11:64004892-64005127236VEGFB_HUMAN137-207710--
1.7ENST000003094227ENSE00001786303chr11:64005828-64006258431VEGFB_HUMAN-00--

(-) 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:96
 aligned with VEGFB_HUMAN | P49765 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:96
                                    43        53        63        73        83        93       103       113       123      
          VEGFB_HUMAN    34 KVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 129
               SCOP domains d2c7wa_ A: automated matches                                                                     SCOP domains
               CATH domains 2c7wA00 A:13-108 Cystine-knot cytokines                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...hhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhh..eeeeeeee.......eeee...eeeeeeeeeeee....eeeeeeeeeee..eeee... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eee------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: A:13-108 UniProt: 34-129                                                            PROSITE (1)
                PROSITE (2) ------------------------------------PDGF_1       ----------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.-----------------------------------------------------------------Exon 1.4  PDB: A:80-104  ---- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: A:14-79 UniProt: 35-100                            ------------------------1.5   Transcript 1 (2)
                 2c7w A  13 KVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 108
                                    22        32        42        52        62        72        82        92       102      


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with VEGFB_HUMAN | P49765 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:96
                                    43        53        63        73        83        93       103       113       123      
          VEGFB_HUMAN    34 KVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 129
               SCOP domains d2c7wb_ B: automated matches                                                                     SCOP domains
               CATH domains 2c7wB00 B:13-108 Cystine-knot cytokines                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ...hhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhh..eeeeeeee.......eeee...eeeeeeeeeeee....eeeeeeeeeee..eeee... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eee------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: B:13-108 UniProt: 34-129                                                            PROSITE (1)
                PROSITE (2) ------------------------------------PDGF_1       ----------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.-----------------------------------------------------------------Exon 1.4  PDB: B:80-104  ---- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: B:14-79 UniProt: 35-100                            ------------------------1.5   Transcript 1 (2)
                 2c7w B  13 KVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 108
                                    22        32        42        52        62        72        82        92       102
   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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C7W)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VEGFB_HUMAN | P49765)
molecular function
    GO:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    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.
    GO:0043183    vascular endothelial growth factor receptor 1 binding    Interacting selectively and non-covalently with vascular endothelial growth factor receptor 1.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0060048    cardiac muscle contraction    Muscle contraction of cardiac muscle tissue.
    GO:0060976    coronary vasculature development    The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0050930    induction of positive chemotaxis    Any process that initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0060754    positive regulation of mast cell chemotaxis    Any process that increases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0043117    positive regulation of vascular permeability    Any process that increases the extent to which blood vessels can be pervaded by fluid.
    GO:0035470    positive regulation of vascular wound healing    Any process that increases the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature.
    GO:0006493    protein O-linked glycosylation    A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan.
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VEGFB_HUMAN | P49765: 2vwe 2xac

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2C7W)