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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE BINDING OF VEGF-B BY VEGFR-1D2: RECOGNITION AND SPECIFICITY
 
Authors :  S. Iyer, P. Darley, K. R. Acharya
Date :  30 Mar 10  (Deposition) - 19 May 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A,B,C,X
Keywords :  Transferase-Signaling Protein Complex, Angiogenesis, Cysteine-Knot Protein, Mitogen, Transferase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Iyer, P. Darley, K. R. Acharya
Structural Insights Into The Binding Of Vegf-B By Vegfr-1D2: Recognition And Specificity
J. Biol. Chem. V. 285 23779 2010
PubMed-ID: 20501651  |  Reference-DOI: 10.1074/JBC.M110.130658

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-32 XA/LIC
    Expression System StrainROSETTAGAMI B (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRECEPTOR-BINDING DOMAIN, RESIDUES 31-129
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVEGF-B, VEGF-RELATED FACTOR, VRF
 
Molecule 2 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
    ChainsC, X
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3) CODONPLUS-RIPL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDOMAIN 2, RESIDUES 129-226
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVEGFR-1, VASCULAR PERMEABILITY FACTOR RECEPTOR, TYROSINE-PROTEIN KINASE RECEPTOR FLT, TYROSINE-PROTEIN KINASE FRT, FLT-1, FMS-LIKE TYROSINE KINASE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCX

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:73 , HIS A:74 , SER A:99 , HOH A:2009 , GLN B:73 , HIS B:74 , SER B:99BINDING SITE FOR RESIDUE GOL B1109

(-) SS Bonds  (10, 10)

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
9C:158 -C:207
10X:158 -X:207

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Val A:48 -Pro A:49
2Val B:48 -Pro B:49
3Tyr B:85 -Pro B:86
4Phe C:172 -Pro C:173
5Phe X:172 -Pro X:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042046E144KVGFR1_HUMANPolymorphism55974987C/XE144K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) 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   (8, 15)

Asymmetric/Biological Unit (8, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002823971ENSE00001249591chr13:29069232-29068917316VGFR1_HUMAN1-22220--
1.2ENST000002823972ENSE00000938500chr13:29041754-2904165897VGFR1_HUMAN22-54330--
1.3ENST000002823973ENSE00000938501chr13:29041266-29041040227VGFR1_HUMAN54-130771C:129-130
-
2
-
1.4ENST000002823974ENSE00000906630chr13:29012482-29012358125VGFR1_HUMAN130-171422C:130-171
X:132-171
42
40
1.5ENST000002823975ENSE00000906629chr13:29008357-29008195163VGFR1_HUMAN172-226552C:172-226
X:172-226
55
55
1.6ENST000002823976ENSE00000906628chr13:29008092-29007956137VGFR1_HUMAN226-271462C:226-226
X:226-226
1
1
1.7ENST000002823977ENSE00000906627chr13:29005447-29005273175VGFR1_HUMAN272-330590--
1.8ENST000002823978ENSE00000906626chr13:29004304-29004187118VGFR1_HUMAN330-369400--
1.9ENST000002823979ENSE00000906625chr13:29002058-29001889170VGFR1_HUMAN369-426580--
1.10ENST0000028239710ENSE00000906624chr13:29001455-29001296160VGFR1_HUMAN426-479540--
1.11ENST0000028239711ENSE00000679737chr13:28980031-28979917115VGFR1_HUMAN479-517390--
1.12ENST0000028239712ENSE00000679735chr13:28971205-28971097109VGFR1_HUMAN518-554370--
1.13ENST0000028239713ENSE00001005702chr13:28964241-28963933309VGFR1_HUMAN554-6571040--
1.14ENST0000028239714ENSE00001005684chr13:28959168-28959022147VGFR1_HUMAN657-706500--
1.15ENST0000028239715ENSE00001005678chr13:28931822-28931691132VGFR1_HUMAN706-750450--
1.16ENST0000028239716ENSE00001005688chr13:28919688-28919582107VGFR1_HUMAN750-785360--
1.17ENST0000028239717ENSE00000679727chr13:28913437-28913305133VGFR1_HUMAN786-830450--
1.18ENST0000028239718ENSE00001005682chr13:28908266-28908162105VGFR1_HUMAN830-865360--
1.19ENST0000028239719ENSE00000679725chr13:28903865-28903752114VGFR1_HUMAN865-903390--
1.20ENST0000028239720ENSE00001005685chr13:28901687-2890159989VGFR1_HUMAN903-932300--
1.21ENST0000028239721ENSE00000679723chr13:28897083-28896927157VGFR1_HUMAN933-985530--
1.22ENST0000028239722ENSE00000679722chr13:28896496-2889639998VGFR1_HUMAN985-1017330--
1.23ENST0000028239723ENSE00001761843chr13:28895722-28895600123VGFR1_HUMAN1018-1058410--
1.24ENST0000028239724ENSE00000679720chr13:28893671-28893560112VGFR1_HUMAN1059-1096380--
1.25ENST0000028239725ENSE00001005671chr13:28891734-28891635100VGFR1_HUMAN1096-1129340--
1.26ENST0000028239726ENSE00001005693chr13:28886235-28886130106VGFR1_HUMAN1129-1164360--
1.27ENST0000028239727ENSE00000679717chr13:28885869-28885727143VGFR1_HUMAN1165-1212480--
1.28ENST0000028239728ENSE00001005655chr13:28883064-2888298085VGFR1_HUMAN1212-1240290--
1.29ENST0000028239729ENSE00000679715chr13:28880909-2888081595VGFR1_HUMAN1241-1272320--
1.30ENST0000028239730ENSE00001157319chr13:28877505-288744893017VGFR1_HUMAN1272-1338670--

2.1ENST000003094221ENSE00001238390chr11:64002266-64002365100VEGFB_HUMAN1-20200--
2.2ENST000003094222ENSE00001238372chr11:64002930-6400297243VEGFB_HUMAN21-35152A:10-14
B:11-14
5
4
2.3ENST000003094223ENSE00001195939chr11:64003285-64003481197VEGFB_HUMAN35-100662A:14-79
B:14-79
66
66
2.4ENST000003094224ENSE00001195931chr11:64003726-6400379974VEGFB_HUMAN101-125252A:80-104
B:80-104
25
25
2.5ENST000003094225ENSE00001195925chr11:64004659-6400469436VEGFB_HUMAN125-137132A:104-108
B:104-108
5
5
2.6aENST000003094226aENSE00001238383chr11:64004892-64005127236VEGFB_HUMAN137-207710--
2.7ENST000003094227ENSE00001786303chr11:64005828-64006258431VEGFB_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:99
 aligned with VEGFB_HUMAN | P49765 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:99
                                    40        50        60        70        80        90       100       110       120         
          VEGFB_HUMAN    31 HQRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 129
               SCOP domains d2xaca_ A: automated matches                                                                        SCOP domains
               CATH domains 2xacA00 A:10-108 Cystine-knot cytokines                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhh..eeeeeeee...........eee..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PDGF_2  PDB: A:13-108 UniProt: 34-129                                                            PROSITE (1)
                PROSITE (2) ---------------------------------------PDGF_1       ----------------------------------------------- PROSITE (2)
           Transcript 2 (1) 2.2  -----------------------------------------------------------------Exon 2.4  PDB: A:80-104  ---- Transcript 2 (1)
           Transcript 2 (2) ----Exon 2.3  PDB: A:14-79 UniProt: 35-100                            ------------------------2.5   Transcript 2 (2)
                 2xac A  10 HQRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 108
                                    19        29        39        49        59        69        79        89        99         

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with VEGFB_HUMAN | P49765 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:98
                                    41        51        61        71        81        91       101       111       121        
          VEGFB_HUMAN    32 QRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 129
               SCOP domains d2xacb_ B: automated matches                                                                       SCOP domains
               CATH domains 2xacB00 B:11-108 Cystine-knot cytokines                                                            CATH domains
           Pfam domains (1) ---------------PDGF-2xacB01 B:26-103                                                         ----- Pfam domains (1)
           Pfam domains (2) ---------------PDGF-2xacB02 B:26-103                                                         ----- Pfam domains (2)
         Sec.struct. author .....hhhhhhhh...eeeeeeee..........eeee..eeeeeeee.......eeeeeeeeee....eeeee.....ee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDGF_2  PDB: B:13-108 UniProt: 34-129                                                            PROSITE (1)
                PROSITE (2) --------------------------------------PDGF_1       ----------------------------------------------- PROSITE (2)
           Transcript 2 (1) 2.2 -----------------------------------------------------------------Exon 2.4  PDB: B:80-104  ---- Transcript 2 (1)
           Transcript 2 (2) ---Exon 2.3  PDB: B:14-79 UniProt: 35-100                            ------------------------2.5   Transcript 2 (2)
                 2xac B  11 QRKVVSWIDVYTRATCQPREVVVPLTVELMGTVAKQLVPSCVTVQRCGGCCPDDGLECVPTGQHQVRMQILMIRYPSSQLGEMSLEEHSQCECRPKKK 108
                                    20        30        40        50        60        70        80        90       100        

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with VGFR1_HUMAN | P17948 from UniProtKB/Swiss-Prot  Length:1338

    Alignment length:98
                                   138       148       158       168       178       188       198       208       218        
          VGFR1_HUMAN   129 SDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT 226
               SCOP domains d2xacc_ C: automated matches                                                                       SCOP domains
               CATH domains 2xacC00 C:129-226 Immunoglobulins                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee......eee...........ee......................eee...hhhhh.eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------K---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.-----------------------------------------Exon 1.5  PDB: C:172-226 UniProt: 172-226               Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4  PDB: C:130-171 UniProt: 130-171 ------------------------------------------------------1 Transcript 1 (2)
                 2xac C 129 SDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT 226
                                   138       148       158       168       178       188       198       208       218        

Chain X from PDB  Type:PROTEIN  Length:95
 aligned with VGFR1_HUMAN | P17948 from UniProtKB/Swiss-Prot  Length:1338

    Alignment length:95
                                   141       151       161       171       181       191       201       211       221     
          VGFR1_HUMAN   132 GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT 226
               SCOP domains d2xacx_ X: automated matches                                                                    SCOP domains
               CATH domains 2xacX00 X:132-226 Immunoglobulins                                                               CATH domains
           Pfam domains (1) -----Ig_2-2xacX01 X:137-226                                                                     Pfam domains (1)
           Pfam domains (2) -----Ig_2-2xacX02 X:137-226                                                                     Pfam domains (2)
         Sec.struct. author ............eeee......eee...........eeee...eee......eeee...eeee........eeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------K---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ----------------------------------------Exon 1.5  PDB: X:172-226 UniProt: 172-226               Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: X:132-171 [INCOMPLETE]   ------------------------------------------------------1 Transcript 1 (2)
                 2xac X 132 GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT 226
                                   141       151       161       171       181       191       201       211       221     

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Family: PDGF (19)
(-)
Clan: Ig (577)
(-)
Family: Ig_2 (52)
2aIg_2-2xacX01X:137-226
2bIg_2-2xacX02X:137-226

(-) Gene Ontology  (81, 88)

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.

Chain C,X   (VGFR1_HUMAN | P17948)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0036326    VEGF-A-activated receptor activity    Combining with vascular endothelial growth factor A (VEGF-A) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    GO:0036327    VEGF-B-activated receptor activity    Combining with vascular endothelial growth factor B (VEGF-B) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0036332    placental growth factor-activated receptor activity    Combining with placental growth factor (PlGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
    GO:0005021    vascular endothelial growth factor-activated receptor activity    Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048514    blood vessel morphogenesis    The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood.
    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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0035924    cellular response to vascular endothelial growth factor 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 vascular endothelial growth factor stimulus.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0048598    embryonic morphogenesis    The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0002548    monocyte chemotaxis    The movement of a monocyte in response to an external stimulus.
    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:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    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:0043552    positive regulation of phosphatidylinositol 3-kinase activity    Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0010863    positive regulation of phospholipase C activity    Any process that increases the rate of phospholipase C activity.
    GO:0048661    positive regulation of smooth muscle cell proliferation    Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
    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:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006940    regulation of smooth muscle contraction    Any process that modulates the frequency, rate or extent of smooth muscle contraction.
    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:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    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.
    GO:0036323    vascular endothelial growth factor receptor-1 signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-1 (VEGFR-1) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0038084    vascular endothelial growth factor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

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

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        VEGFB_HUMAN | P497652c7w 2vwe
        VGFR1_HUMAN | P179481flt 1qsv 1qsz 1qty 1rv6 3hng 4ckv 4cl7 5abd 5ex3 5t89

(-) Related Entries Specified in the PDB File

1flt VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT -1 RECEPTOR
1qsv THE VEGF-BINDING DOMAIN OF FLT-1, 20 NMR STRUCTURES
1qsz THE VEGF-BINDING DOMAIN OF FLT-1 ( MINIMIZED MEAN)
1qty VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR
1rv6 CRYSTAL STRUCTURE OF PLGF IN COMPLEX WITH DOMAIN 2 OF VEGFR1
2c7w CRYSTAL STRUCTURE OF HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR-B: IDENTIFICATION OF AMINO ACIDS IMPORTANT FOR ANGIOGENINC ACTIVITY
2vwe CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR-B IN COMPLEX WITH A NEUTRALIZING ANTIBODY FAB FRAGMENT