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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARF6 GTPASE IN COMPLEX WITH A SPECIFIC EFFECTOR, JIP4
 
Authors :  T. Isabet, G. Montagnac, K. Regazzoni, B. Raynal, F. El Khadali, M. Franco, P. England, P. Chavrier, A. Houdusse, J. Menetrey
Date :  08 Jan 09  (Deposition) - 14 Jul 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Golgi Apparatus, Protein Transport, Er-Golgi Transport, Arf, Gtpase, Effector, Myristate, Cytoplasm, Nucleotide-Binding, Alternative Splicing, Gtp-Binding, Phosphoprotein, Heterotetramer, Transport, Coiled-Coil, Lipoprotein, Coiled Coil (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Isabet, G. Montagnac, K. Regazzoni, B. Raynal, F. El Khadali, P. England, M. Franco, P. Chavrier, A. Houdusse, J. Menetrey
The Structural Basis Of Arf Effector Specificity: The Crystal Structure Of Arf6 In A Complex With Jip4.
Embo J. V. 28 2835 2009
PubMed-ID: 19644450  |  Reference-DOI: 10.1038/EMBOJ.2009.209

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR 6
    Chains: A, B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: G DOMAIN, RESIDUES 13-175
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: 12 RESIDUES N-TERMINAL DELETION
    Synonym: ARF6
 
Molecule 2 - C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 4
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGST
    Fragment: LEUCINE ZIPPER II, RESIDUES 392-462
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JIP4, JNK-INTERACTING PROTEIN 4, JIP-4, JLP, HLC-6, PHET, CT89, JNK-ASSOCIATED LEUCINE-ZIPPER PROTEIN, SPERM-ASSOCIATED ANTIGEN 9, MITOGEN-ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 4, HUMAN LUNG CANCER ONCOGENE 6 PROTEIN, PROLIFERATION-INDUCING PROTEIN 6, SPERM-SPECIFIC PROTEIN, SPERM SURFACE PROTEIN, PROTEIN HIGHLY EXPRESSED IN TESTIS, SUNDAY DRIVER 1, CANCER/TESTIS ANTIGEN 89

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1DIO6Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL1Ligand/IonGLYCEROL
3GTP3Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
4MG3Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:22 , ALA A:23 , ALA A:24 , GLY A:25 , LYS A:26 , THR A:27 , THR A:28 , THR A:41 , PRO A:43 , THR A:44 , GLY A:65 , GLY A:66 , ASN A:122 , LYS A:123 , ASP A:125 , LEU A:126 , CYS A:155 , ALA A:156 , MG A:1174 , HOH A:2011 , HOH A:2033 , HOH A:2093 , HOH A:2094 , HOH A:2095 , HOH A:2096 , HOH A:2097 , HOH A:2098BINDING SITE FOR RESIDUE GTP A1173
02AC2SOFTWARETHR A:27 , THR A:44 , GTP A:1173 , HOH A:2033 , HOH A:2094BINDING SITE FOR RESIDUE MG A1174
03AC3SOFTWAREASP B:22 , ALA B:23 , ALA B:24 , GLY B:25 , LYS B:26 , THR B:27 , THR B:28 , THR B:41 , PRO B:43 , THR B:44 , GLY B:66 , ASN B:122 , LYS B:123 , ASP B:125 , CYS B:155 , ALA B:156 , THR B:157 , MG B:1174 , HOH B:2007 , HOH B:2015 , HOH B:2029BINDING SITE FOR RESIDUE GTP B1173
04AC4SOFTWARETHR B:27 , THR B:44 , GTP B:1173 , HOH B:2007 , HOH B:2015BINDING SITE FOR RESIDUE MG B1174
05AC5SOFTWAREASP E:22 , ALA E:23 , ALA E:24 , GLY E:25 , LYS E:26 , THR E:27 , THR E:28 , THR E:41 , PRO E:43 , THR E:44 , GLY E:65 , GLY E:66 , ASN E:122 , LYS E:123 , ASP E:125 , LEU E:126 , CYS E:155 , ALA E:156 , THR E:157 , MG E:1174 , HOH E:2014 , HOH E:2029 , HOH E:2083 , HOH E:2084 , HOH E:2085 , HOH E:2086 , HOH E:2088 , HOH E:2089BINDING SITE FOR RESIDUE GTP E1173
06AC6SOFTWARETHR E:27 , THR E:44 , GTP E:1173 , HOH E:2029 , HOH E:2083BINDING SITE FOR RESIDUE MG E1174
07AC7SOFTWAREPRO A:132 , HIS A:133 , GLN A:136 , GLN E:136BINDING SITE FOR RESIDUE DIO A1175
08AC8SOFTWAREPRO A:132 , HIS A:133 , LYS E:131 , PRO E:132 , HIS E:133BINDING SITE FOR RESIDUE DIO E1175
09AC9SOFTWAREILE A:70 , THR C:404 , ILE C:415 , DIO C:1454 , LEU D:399 , GLU D:402BINDING SITE FOR RESIDUE DIO C1453
10BC1SOFTWARELYS A:69 , LEU A:73 , GLU C:408 , ALA C:412 , DIO C:1453BINDING SITE FOR RESIDUE DIO C1454
11BC2SOFTWAREPHE C:391 , THR E:27 , LYS E:34 , LEU E:35 , THR E:41 , ILE E:42BINDING SITE FOR RESIDUE DIO E1176
12BC3SOFTWARELEU D:407 , ASN D:411 , LYS E:69 , ILE E:70 , LEU E:73BINDING SITE FOR RESIDUE DIO E1177
13BC4SOFTWAREARG A:71 , PRO A:72 , TRP A:74 , ARG A:75 , TYR A:78 , GLU A:102 , ARG A:105 , HOH A:2099BINDING SITE FOR RESIDUE GOL A1176

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W83)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W83)

(-) Exons   (1, 3)

Asymmetric/Biological Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002983161ENSE00001093805chr14:50359810-5035987566ARF6_HUMAN-00--
1.2ENST000002983162ENSE00001093803chr14:50359974-503614901517ARF6_HUMAN1-3363363A:12-172
B:12-172
E:11-172		161
161
162

(-) 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:161
 aligned with ARF6_HUMAN | P62330 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:161
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
           ARF6_HUMAN    12 KEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSN 172
               SCOP domains d2w83a_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 2w83A00 A:12-172 P-loop containing nucleotide triphosphate hydrolases                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh..........eeeeeeee..eeeeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh...hhhhh....eeeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:12-172 UniProt: 1-336 [INCOMPLETE]                                                                                                               Transcript 1
                 2w83 A  12 MEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSN 172
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with ARF6_HUMAN | P62330 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:161
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
           ARF6_HUMAN    12 KEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSN 172
               SCOP domains d2w83b_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains 2w83B00 B:12-172 P-loop containing nucleotide triphosphate hydrolases                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh..........eeeeeee....eeeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhh.........eeeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:12-172 UniProt: 1-336 [INCOMPLETE]                                                                                                               Transcript 1
                 2w83 B  12 MEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSN 172
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 


Chain C from PDB  Type:PROTEIN  Length:67
 aligned with JIP4_HUMAN | O60271 from UniProtKB/Swiss-Prot  Length:1321

    Alignment length:115
                                   361       371       381       391       401       411       421       431       441       451       461     
           JIP4_HUMAN   352 DMDKDLSGYKGSSTPTKGIENKAFDRNTESLFEELSSAGSGLIGDVDEGADLLGMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKN 466
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w83C0                                                0 C:386-452                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2w83 C 386 AMDPEF------------------------------------------------MGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKN 452
                                 |   -         -         -         -         -    |  397       407       417       427       437       447     
                               391                                              392                                                            


Chain D from PDB  Type:PROTEIN  Length:62
 aligned with JIP4_HUMAN | O60271 from UniProtKB/Swiss-Prot  Length:1321

    Alignment length:62
                                   414       424       434       444       454       464  
           JIP4_HUMAN   405 GMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKN 466
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains 2w83D00 D:391-452                                              CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 2w83 D 391 FMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKN 452
                                   400       410       420       430       440       450  


Chain E from PDB  Type:PROTEIN  Length:162
 aligned with ARF6_HUMAN | P62330 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:162
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           ARF6_HUMAN    11 NKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSN 172
               SCOP domains d2w83e_ E: automated matches                                                                                                                                       SCOP domains
               CATH domains 2w83E00 E:11-172 P-loop containing nucleotide triphosphate hydrolases                                                                                              CATH domains
           Pfam domains (1) --Arf-2w83E01 E:13-172                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --Arf-2w83E02 E:13-172                                                                                                                                             Pfam domains (2)
           Pfam domains (3) --Arf-2w83E03 E:13-172                                                                                                                                             Pfam domains (3)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..........eeeeeeee..eeeeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: E:11-172 UniProt: 1-336 [INCOMPLETE]                                                                                                                Transcript 1
                 2w83 E  11 AMEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLTSN 172
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Arf (26)
(-)
Homo sapiens (Human) (9)
1aArf-2w83E01E:13-172
1bArf-2w83E02E:13-172
1cArf-2w83E03E:13-172

(-) Gene Ontology  (73, 76)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,E   (ARF6_HUMAN | P62330)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0031996    thioesterase binding    Interacting selectively and non-covalently with any thioesterase enzyme.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    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:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0030866    cortical actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane.
    GO:0090162    establishment of epithelial cell polarity    The specification and formation of anisotropic intracellular organization of an epithelial cell.
    GO:0097284    hepatocyte apoptotic process    Any apoptotic process in a hepatocyte, the main structural component of the liver.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0033028    myeloid cell apoptotic process    Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
    GO:2000171    negative regulation of dendrite development    Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite development.
    GO:0048261    negative regulation of receptor-mediated endocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0090004    positive regulation of establishment of protein localization to plasma membrane    Any process that increases the frequency, rate or extent of the directed movement of a protein to a specific location in the plasma membrane.
    GO:0034394    protein localization to cell surface    A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
    GO:0036010    protein localization to endosome    A process in which a protein is transported to, or maintained in, a location within an endosome.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0035020    regulation of Rac protein signal transduction    Any process that modulates the frequency, rate or extent of Rac protein signal transduction.
    GO:0060998    regulation of dendritic spine development    Any process that modulates the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:0051489    regulation of filopodium assembly    Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0031529    ruffle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
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:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031527    filopodium membrane    The portion of the plasma membrane surrounding a filopodium.
    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: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:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    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:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

Chain C,D   (JIP4_HUMAN | O60271)
molecular function
    GO:0008432    JUN kinase binding    Interacting selectively and non-covalently with JUN kinase, an enzyme that catalyzes the phosphorylation and activation of members of the JUN family.
    GO:0005078    MAP-kinase scaffold activity    The binding activity of a molecule that functions as a physical support for the assembly of a multiprotein mitogen-activated protein kinase (MAPK) complex. Binds multiple kinases of the MAPKKK cascade, and also upstream signaling proteins, permitting those molecules to function in a coordinated way. Bringing together multiple enzymes and their substrates enables the signal to be transduced quickly and efficiently.
    GO:0019894    kinesin binding    Interacting selectively and non-covalently and stoichiometrically with kinesin, a member of a superfamily of microtubule-based motor proteins that perform force-generating tasks such as organelle transport and chromosome segregation.
    GO:0048273    mitogen-activated protein kinase p38 binding    Interacting selectively and non-covalently with mitogen-activated protein kinase p38, an enzyme that catalyzes the transfer of phosphate from ATP to hydroxyl side chains on proteins in response to mitogen activation.
    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:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
biological process
    GO:0007257    activation of JUN kinase activity    The initiation of the activity of the inactive enzyme JUN kinase (JNK).
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0090074    negative regulation of protein homodimerization activity    Any process that decreases the frequency, rate or extent of protein homodimerization, interacting selectively with an identical protein to form a homodimer.
    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:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0042147    retrograde transport, endosome to Golgi    The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0051146    striated muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle.
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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  2w83
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  ARF6_HUMAN | P62330
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  JIP4_HUMAN | O60271
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARF6_HUMAN | P62330: 1e0s 2a5d 2a5f 2a5g 2bao 2bau 2j5x 3lvq 3lvr 3n5c 3pcr 4fme 4kax

(-) Related Entries Specified in the PDB File

1e0s SMALL G PROTEIN ARF6-GDP
2a5d STRUCTURAL BASIS FOR THE ACTIVATION OF CHOLERA TOXIN BYHUMAN ARF6-GTP
2a5f CHOLERA TOXIN A1 SUBUNIT BOUND TO ITS SUBSTRATE, NAD+, ANDITS HUMAN PROTEIN ACTIVATOR, ARF6
2a5g CHOLERA TOXIN A1 SUBUNIT BOUND TO ARF6( Q67L)
2j5x STRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS