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(-) Description

Title :  STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 10B
 
Authors :  J. Choe, A. Atanassova, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  14 Apr 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Transport Protein, Gdp-Binding, Membrane Trafficking, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Atanassova, J. Choe, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park
Structure Of Human Adp-Ribosylation Factor-Like 10B
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-RIBOSYLATION FACTOR-LIKE 10B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:33 , GDP A:201 , HOH A:322 , HOH A:337 , HOH A:382 , HOH A:400BINDING SITE FOR RESIDUE MG A 202
2AC2SOFTWARETYR A:29 , SER A:30 , GLY A:31 , LYS A:32 , THR A:33 , THR A:34 , PHE A:44 , ASN A:45 , GLU A:46 , MET A:48 , ASN A:129 , LYS A:130 , ASP A:132 , LEU A:133 , SER A:162 , CYS A:163 , LYS A:164 , MG A:202 , HOH A:376 , HOH A:382 , HOH A:396 , HOH A:400 , HOH A:401BINDING SITE FOR RESIDUE GDP A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZD9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZD9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZD9)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002722171ENSE00001074706chr1:202113869-202113578292ARL8A_HUMAN1-41411A:16-4025
1.2ENST000002722172ENSE00000962395chr1:202107576-20210749681ARL8A_HUMAN42-68271A:41-6727
1.3aENST000002722173aENSE00000962396chr1:202107166-20210709374ARL8A_HUMAN69-93251A:68-9225
1.4aENST000002722174aENSE00000962397chr1:202104928-20210483594ARL8A_HUMAN93-124321A:92-12332
1.4dENST000002722174dENSE00000962398chr1:202104654-20210458768ARL8A_HUMAN125-147231A:124-14623
1.5bENST000002722175bENSE00001687069chr1:202104348-20210427871ARL8A_HUMAN147-171251A:146-17025
1.6bENST000002722176bENSE00001191671chr1:202103644-2021025321113ARL8A_HUMAN171-186161A:170-18112

(-) 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:166
 aligned with ARL8A_HUMAN | Q96BM9 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:166
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      
          ARL8A_HUMAN    17 WKEEMELTLVGLQYSGKTTFVNVIASGQFNEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPGALDEKELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSK 182
               SCOP domains --d1zd9a1 A:18-181 ADP-ribosylation factor                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh...........eeeeeeee..eeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:16-40   Exon 1.2  PDB: A:41-67     Exon 1.3a  PDB: A:68-92  -------------------------------Exon 1.4d              -----------------------Exon 1.6b    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.4a  PDB: A:92-123        ----------------------Exon 1.5b  PDB: A:146-170----------- Transcript 1 (2)
                 1zd9 A  16 SKEEMELTLVGLQYSGKTTFVNVIASGQFNEDMIPTVGFNMRKITKGNVTIKLWDIGGQPRFRSMWERYCRGVSAIVYMVDAADQEKIEASKNELHNLLDKPQLQGIPVLVLGNKRDLPGALDEKELIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSK 181
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      

   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  (0, 0)

(no "CATH Domain" information available for 1ZD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZD9)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARL8A_HUMAN | Q96BM9)
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:0043014    alpha-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein alpha-tubulin.
    GO:0048487    beta-tubulin binding    Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
    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).
biological process
    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: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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    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.
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: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: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:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    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:0051233    spindle midzone    The area in the center of the spindle where the spindle microtubules from opposite poles overlap.

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 Related Entries

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

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        ARL8A_HUMAN | Q96BM92h18 4ile

(-) Related Entries Specified in the PDB File

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