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(-) Description

Title :  CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR D
 
Authors :  V. -M. Leppanen, M. Jeltsch, A. Anisimov, D. Tvorogov, K. Aho, N. Kalkki P. Toivanen, S. Yla-Herttuala, K. Ballmer-Hofer, K. Alitalo
Date :  23 Oct 10  (Deposition) - 12 Jan 11  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Angiogenesis, Lymphangiogenesis, Hormone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. M. Leppanen, M. Jeltsch, A. Anisimov, D. Tvorogov, K. Aho, N. Kalkkinen, P. Toivanen, S. Yla-Herttuala, K. Ballmer-Hofer, K. Alitalo
Structural Determinants Of Vascular Endothelial Growth Factor-D - Receptor Binding And Specificity.
Blood V. 117 1507 2011
PubMed-ID: 21148085  |  Reference-DOI: 10.1182/BLOOD-2010-08-301549

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR D
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System PlasmidPFASTBAC
    Expression System StrainSF21
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentVEGF HOMOLOGY DOMAIN, RESIDUES 92-195
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsN-GLYCOSYLATION AT ASN155 AND ASN185.
    SynonymC-FOS-INDUCED GROWTH FACTOR, VEGF-D, FIGF

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREBMA A:402BINDING SITE FOR RESIDUE MAN A 403
2AC2SOFTWARELEU A:124 , GLY A:125 , BMA A:402BINDING SITE FOR RESIDUE MAN A 404
3AC3SOFTWAREASN A:155 , THR A:158 , TYR A:160 , ALA A:184 , HIS A:186 , MAN A:403 , MAN A:404 , HOH A:2010 , HOH A:2011 , HOH A:2012 , HOH A:2013BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 155 RESIDUES 400 TO 402
4AC4SOFTWAREPRO A:113 , PHE A:140 , SER A:159 , ILE A:161 , ASN A:185 , HIS A:186 , THR A:187BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 185 RESIDUES 500 TO 502

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:111 -A:153
2A:136 -A:145
3A:142 -A:189
4A:146 -A:191

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Lys A:133 -Pro A:134
2Val A:170 -Pro A:171
3Pro A:171 -Leu A:172
4Thr A:173 -Ser A:174
5Pro A:193 -Thr A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XV7)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.VEGFD_HUMAN97-196  1A:97-194
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.VEGFD_HUMAN134-146  1A:134-146
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.VEGFD_HUMAN97-196  2A:97-194
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.VEGFD_HUMAN134-146  2A:134-146

(-) Exons   (0, 0)

(no "Exon" information available for 2XV7)

(-) 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    
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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:104
 aligned with VEGFD_HUMAN | O43915 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:104
                                   100       110       120       130       140       150       160       170       180       190    
          VEGFD_HUMAN    91 ATFYDIETLKVIDEEWQRTQCSPRETCVEVASELGKSTNTFFKPPCVNVFRCGGCCNEESLICMNTSTSYISKQLFEISVPLTSVPELVPVKVANHTGCKCLPT 194
               SCOP domains d2xv7a_ A: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------PDGF-2xv7A01 A:111-191                                                           --- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..eeeeeeee.hhhh.hhhh......eeeeeeee........eeeeeeeeeeeeeee...........eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------PDGF_2  PDB: A:97-194 UniProt: 97-196                                                              PROSITE (1)
                PROSITE (2) -------------------------------------------PDGF_1       ------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 2xv7 A  91 PTFYDIETLKVIDEEWQRTQCSPRETAVEVASELGKSTNTFFKPPCVNVFRCGGCCNEESLICMNTSTSYISKQLFEISVPLTSVPELVPVKVANHTGCKCLPT 194
                                   100       110       120       130       140       150       160       170       180       190    

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  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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XV7)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A   (VEGFD_HUMAN | O43915)
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:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043185    vascular endothelial growth factor receptor 3 binding    Interacting selectively and non-covalently with vascular endothelial growth factor receptor 3.
    GO:0005172    vascular endothelial growth factor receptor binding    Interacting selectively and non-covalently with any vascular endothelial growth factor receptor.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0071542    dopaminergic neuron differentiation    The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine.
    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: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: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: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:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    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:0030947    regulation of vascular endothelial growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    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:0070555    response to interleukin-1    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 an interleukin-1 stimulus.
    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.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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