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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH A PYRIDINYL-TRIAZINE INHIBITOR
 
Authors :  D. A. Whittington, J. L. Kim, A. M. Long, P. Rose, Y. Gu, H. Zhao
Date :  07 Mar 07  (Deposition) - 20 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Receptor Tyrosine Kinase, Kdr, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. L. Hodous, S. D. Geuns-Meyer, P. E. Hughes, B. K. Albrecht, S. Bellon, J. Bready, S. Caenepeel, V. J. Cee, S. C. Chaffee, A. Coxon, M. Emery, J. Fretland, P. Gallant, Y. Gu, D. Hoffman, R. E. Johnson, R. Kendall, J. L. Kim, A. M. Long, M. Morrison, P. R. Olivieri, V. F. Patel, A. Polverino, P. Rose, P. Tempest, L. Wang, D. A. Whittington, H. Zhao
Evolution Of A Highly Selective And Potent 2-(Pyridin-2-Yl)-1, 3, 5-Triazine Tie-2 Kinase Inhibitor
J. Med. Chem. V. 50 611 2007
PubMed-ID: 17253678  |  Reference-DOI: 10.1021/JM061107L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentKINASE DOMAIN
    GeneKDR, FLK1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVEGFR-2, KINASE INSERT DOMAIN RECEPTOR, PROTEIN- TYROSINE KINASE RECEPTOR FLK-1, CD309 ANTIGEN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
19941Ligand/Ion4-(2-ANILINOPYRIDIN-3-YL)-N-(3,4,5-TRIMETHOXYPHENYL)-1,3,5-TRIAZIN-2-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:61 , VAL A:848 , ALA A:866 , LYS A:868 , GLU A:885 , THR A:916 , GLU A:917 , PHE A:918 , CYS A:919 , LYS A:920 , PHE A:921 , GLY A:922 , LEU A:1035 , CYS A:1045BINDING SITE FOR RESIDUE 994 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P2H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:991 -Pro A:992

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_046679V848EVGFR2_HUMANPolymorphism1139776AV848E
2UniProtVAR_036127G873RVGFR2_HUMANUnclassified  ---AG873R
3CancerSNPVAR_VGFR2_HUMAN_CCDS3497_1_02 *G873RVGFR2_HUMANDisease (Colorectal cancer)  ---AG873R
4UniProtVAR_063147P1147SVGFR2_HUMANDisease (HCI)121917766AP1147S
   * ID not provided by source

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.VGFR2_HUMAN840-868  1A:840-868
2RECEPTOR_TYR_KIN_IIIPS00240 Receptor tyrosine kinase class III signature.VGFR2_HUMAN893-906  1A:893-906
3PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.VGFR2_HUMAN1024-1036  1A:1024-1036

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002639231aENSE00001171700chr4:55991756-55991394363VGFR2_HUMAN1-23230--
1.2ENST000002639232ENSE00000716050chr4:55987357-5598726494VGFR2_HUMAN23-54320--
1.3ENST000002639233ENSE00000716047chr4:55984967-55984771197VGFR2_HUMAN54-120670--
1.4ENST000002639234ENSE00000716045chr4:55981578-55981448131VGFR2_HUMAN120-163440--
1.5ENST000002639235ENSE00000716043chr4:55981209-55981041169VGFR2_HUMAN164-220570--
1.6ENST000002639236ENSE00000716040chr4:55980432-55980293140VGFR2_HUMAN220-266470--
1.7ENST000002639237ENSE00000716038chr4:55979648-55979471178VGFR2_HUMAN267-326600--
1.8ENST000002639238ENSE00000716036chr4:55976935-55976821115VGFR2_HUMAN326-364390--
1.9ENST000002639239ENSE00000580228chr4:55976733-55976570164VGFR2_HUMAN364-419560--
1.10ENST0000026392310ENSE00000716032chr4:55974060-55973904157VGFR2_HUMAN419-471530--
1.11ENST0000026392311ENSE00000716030chr4:55972977-55972854124VGFR2_HUMAN471-512420--
1.12ENST0000026392312ENSE00000716029chr4:55972107-55971999109VGFR2_HUMAN513-549370--
1.13aENST0000026392313aENSE00001074496chr4:55971151-55970810342VGFR2_HUMAN549-6631150--
1.14ENST0000026392314ENSE00000716025chr4:55968675-55968529147VGFR2_HUMAN663-712500--
1.15ENST0000026392315ENSE00000716023chr4:55968195-55968064132VGFR2_HUMAN712-756450--
1.16ENST0000026392316ENSE00000716022chr4:55964970-55964864107VGFR2_HUMAN756-791360--
1.17ENST0000026392317ENSE00000716020chr4:55964439-55964304136VGFR2_HUMAN792-837461A:815-83723
1.18ENST0000026392318ENSE00000716018chr4:55963933-55963829105VGFR2_HUMAN837-872361A:837-872 (gaps)36
1.19bENST0000026392319bENSE00001312000chr4:55962509-55962396114VGFR2_HUMAN872-910391A:872-91039
1.20ENST0000026392320ENSE00000716016chr4:55961832-5596174489VGFR2_HUMAN910-939301A:910-93930
1.21bENST0000026392321bENSE00000716015chr4:55961122-55960969154VGFR2_HUMAN940-991521A:990-9912
1.22ENST0000026392322ENSE00000877921chr4:55958881-5595878498VGFR2_HUMAN991-1023331A:991-102333
1.23ENST0000026392323ENSE00001608690chr4:55956245-55956123123VGFR2_HUMAN1024-1064411A:1024-105027
1.24ENST0000026392324ENSE00000877919chr4:55955969-55955858112VGFR2_HUMAN1065-1102381A:1066-110237
1.25ENST0000026392325ENSE00000877918chr4:55955640-55955541100VGFR2_HUMAN1102-1135341A:1102-113534
1.26ENST0000026392326ENSE00000877917chr4:55955140-55955035106VGFR2_HUMAN1135-1170361A:1135-117036
1.27ENST0000026392327ENSE00000877916chr4:55953925-55953774152VGFR2_HUMAN1171-1221511A:1171-11755
1.28ENST0000026392328ENSE00000877915chr4:55948802-55948703100VGFR2_HUMAN1221-1254340--
1.29ENST0000026392329ENSE00001148006chr4:55948208-5594812386VGFR2_HUMAN1255-1283290--
1.30ENST0000026392330ENSE00001171693chr4:55946330-559446441687VGFR2_HUMAN1283-1356740--

(-) 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:292
 aligned with VGFR2_HUMAN | P35968 from UniProtKB/Swiss-Prot  Length:1356

    Alignment length:361
                                   824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174 
         VGFR2_HUMAN    815 EHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKTKGARFRQGKDYVGAIPVDLKRRLDSITSSQSSASSGFVEEKSLSDVEEEEAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDGKDY 1175
               SCOP domains d2p2ha_ A: Vascular endothel    ial growth factor receptor 2 (kdr)                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2p2hA01 A:815-918 Phosphoryl    ase Kinase; domain 1                                                    2p2hA02 A:919-1166 Tr                                                  ansferase(Phosphotransferase) domain 1                                                                                                                                           --------- CATH domains
               Pfam domains -------------------Pkinase_T    yr-2p2hA01 A:834-1160                                                                                                                                                                                                                                                                                                     --------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhh.hhh.eeeeeeee.----.eeeeeee.......eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee.......eeeee.....hhhhhhhh.........--------------------------------------------------..hhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.hhh.eee......---------------.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh............hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------E------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------PROTEIN_KINASE_ATP           ------------------------RECEPTOR_TYR_K---------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.17 [INCOMPLETE] ----------------------------------Exon 1.19b  PDB: A:872-910             -----------------------------Exon 1.21b  PDB: A:990-991 UniProt: 940-991         --------------------------------Exon 1.23  PDB: A:1024-1050 [INCOMPLETE] Exon 1.24  PDB: A:1066-1102           --------------------------------Exon 1.26  PDB: A:1135-1170         1.27  Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.18  PDB: A:837-872 (gaps)    -------------------------------------Exon 1.20  PDB: A:910-939     ---------------------------------------------------Exon 1.22  PDB: A:991-1023       ------------------------------------------------------------------------------Exon 1.25  PDB: A:1102-1135       ---------------------------------------- Transcript 1 (2)
                2p2h A  815 EHAERLPYDASKWEFPRDRLKLGKPLGR----QVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNLSTYLRSKRNEFVPYK--------------------------------------------------VAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLA---------------RLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDRHHH 1175
                                   824       834       | -  |    854       864       874       884       894       904       914       924       934    |    -         -         -         -         -     | 994      1004      1014      1024      1034      1044     |   -         - |    1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174 
                                                     842  847                                                                                         939                                                990                                                        1050            1066                                                                                                             

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (68, 68)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VGFR2_HUMAN | P35968)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051879    Hsp90 protein binding    Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
    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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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: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:0004716    signal transducer, downstream of receptor, with protein tyrosine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-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:0038085    vascular endothelial growth factor binding    Interacting selectively and non-covalently with a vascular endothelial growth factor.
    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:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0035584    calcium-mediated signaling using intracellular calcium source    A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response.
    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:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    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:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0003158    endothelium development    The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    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: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:2000352    negative regulation of endothelial cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    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: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: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:0038033    positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a VEGFR on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
    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:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0016239    positive regulation of macroautophagy    Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
    GO:0051901    positive regulation of mitochondrial depolarization    Any process that activates, maintains or increases the frequency, rate or extent of the change in the membrane potential of the mitochondria from negative to positive.
    GO:0090141    positive regulation of mitochondrial fission    Any process that increases the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:0051770    positive regulation of nitric-oxide synthase biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
    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:0050927    positive regulation of positive chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    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:2001214    positive regulation of vasculogenesis    Any process that activates or increases the frequency, rate or extent of vasculogenesis.
    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:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
    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:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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: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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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: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:0097443    sorting endosome    A multivesicular body surrounded by and connected with multiple tubular compartments with associated vesicles.

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 Related Entries

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

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        VGFR2_HUMAN | P359681vr2 1y6a 1y6b 1ywn 2m59 2met 2meu 2oh4 2p2i 2qu5 2qu6 2rl5 2x1w 2x1x 2xir 3b8q 3b8r 3be2 3c7q 3cjf 3cjg 3cp9 3cpb 3cpc 3dtw 3efl 3ewh 3kvq 3s35 3s36 3s37 3u6j 3v2a 3v6b 3vhe 3vhk 3vid 3vnt 3vo3 3wzd 3wze 4ag8 4agc 4agd 4asd 4ase 5ew3

(-) Related Entries Specified in the PDB File

2p2i