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(-) Description

Title :  GDP-BOUND RAB23 GTPASE CRYSTALLIZED IN P2(1)2(1)2(1) SPACE GROUP
 
Authors :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Date :  07 Mar 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Rab Gtpase, Rab23, Vesicular Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Structural Basis Of Family-Wide Rab Gtpase Recognition By Rabenosyn-5.
Nature V. 436 415 2005
PubMed-ID: 16034420  |  Reference-DOI: 10.1038/NATURE03798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-23
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T1
    Expression System StrainBL21 (DE3) CODON PLUS-RIL CELLS
    Expression System Taxid562
    Expression System Vector TypeGST FUSION, PGEX
    GeneRAB23
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 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
1AC1SOFTWARESER A:23 , GDP A:201 , HOH A:310 , HOH A:313 , HOH A:314 , HOH A:324BINDING SITE FOR RESIDUE MG A 300
2AC2SOFTWAREALA A:19 , VAL A:20 , GLY A:21 , LYS A:22 , SER A:23 , SER A:24 , PHE A:34 , ASP A:37 , TYR A:38 , LYS A:40 , ASN A:121 , LYS A:122 , ASP A:124 , SER A:151 , VAL A:152 , LYS A:153 , MG A:300 , HOH A:310 , HOH A:313 , HOH A:314 , HOH A:316 , HOH A:365 , HOH A:383BINDING SITE FOR RESIDUE GDP A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z2A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z2A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z2A)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z2A)

(-) 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:164
 aligned with RAB23_MOUSE | P35288 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:164
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    
          RAB23_MOUSE     8 VAIKMVVVGNGAVGKSSMIQRYCKGIFTKDYKKTIGVDFLERQIQVNDEDVRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEVGDIPTALVQNKIDLLDDSCIKNEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEKHLQ 171
               SCOP domains d1z2aa_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains 1z2aA00 A:8-171 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains ---Ras-1z2aA01 A:11-171                                                                                                                                              Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.............eeeeeeee..eeeeeeee...hhhhh...hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2a A   8 VAIKMVVVGNGAVGKSSMIQRYCKGIFTKDYKKTIGVDFLERQIQVNDEDVRLMLWDTAGQEEFDAITKAYYRGAQACVLVFSTTDRESFEAISSWREKVVAEVGDIPTALVQNKIDLLDDSCIKNEEAEGLAKRLKLRFYRTSVKEDLNVSEVFKYLAEKHLQ 171
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167    

   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB23_MOUSE | P35288)
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.
biological process
    GO:0000045    autophagosome assembly    The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
    GO:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0097094    craniofacial suture morphogenesis    The process in which any suture between cranial and/or facial bones is generated and organized.
    GO:0021904    dorsal/ventral neural tube patterning    The process in which the neural tube is regionalized in the dorsoventral axis.
    GO:0042733    embryonic digit morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
    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:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0042992    negative regulation of transcription factor import into nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
    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:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    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:0008589    regulation of smoothened signaling pathway    Any process that modulates the frequency, rate or extent of smoothened signaling.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving 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:0021513    spinal cord dorsal/ventral patterning    The process that regulates the coordinated growth and differentiation that establishes the non-random dorsal-ventral spatial arrangement of the spinal cord.
    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.
cellular component
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    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.

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 Related Entries

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

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        RAB23_MOUSE | P352881z22

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