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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE VPS26B
 
Authors :  D. J. Owen, R. D. Teasdale, B. M. Collins
Date :  02 Sep 07  (Deposition) - 15 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Retromer, Fibronectin Iii, Arrestin Domain, Membrane, Phosphorylation, Protein Transport, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. M. Collins, S. J. Norwood, M. C. Kerr, D. Mahony, M. N. Seaman, R. D. Teasdale, D. J. Owen
Structure Of Vps26B And Mapping Of Its Interaction With The Retromer Protein Complex.
Traffic V. 9 366 2008
PubMed-ID: 18088321  |  Reference-DOI: 10.1111/J.1600-0854.2007.00688.X

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMWKANH6 MVPS26B
    Expression System StrainBL21 ROSETTA
    Expression System Vector TypePLASMID
    FragmentRESIDUES 7-336
    GeneVPS26B
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    SynonymVESICLE PROTEIN SORTING 26B

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2R51)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R51)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:156 -Glu A:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R51)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R51)

(-) Exons   (0, 0)

(no "Exon" information available for 2R51)

(-) Sequences/Alignments

Asymmetric 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:288
 aligned with VP26B_MOUSE | Q8C0E2 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:288
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288        
          VP26B_MOUSE     9 SVEVEILLNDAESRKRAEHKTEDGKKEKYFLFYDGETVSGKVSLSLKNPNKRLEHQGIKIEFIGQIELYYDRGNHHEFVSLVKDLARPGEITQSQAFDFEFTHVEKPYESYTGQNVKLRYFLRATISRRLNDVVKEMDIVVHTLSTYPELNSSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIKHMEIDIIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGESIPIRLFLAGYELTPTMRDINKKFSVRYYLNLVLIDEEERRYFKQQEVVLWRKG 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Vps26-2r51A01 A:9-281                                                                                                                                                                                                                                                            --------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeee.....eeeeeeee....eeeeeeeee......eee..eeeeeeeeeee.hhh...eeeeeeeeeee..eee...eeeeeee.........ee...eeeeeeeeeee......eeeeeeeeee...........eeeeeee...eeeeeee...eee...eeeeeeeeeee...eeeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.......eeeeeee.hhh.....eeee...eeeeeeeeeeeee....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r51 A   9 SVEVEILLNDAESRKRAEHKTEDGKKEKYFLFYDGETVSGKVSLSLKNPNKRLEHQGIKIEFIGQIELYYDRGNHHEFVSLVKDLARPGEITQSQAFDFEFTHVEKPYESYTGQNVKLRYFLRATISRRLNDVVKEmDIVVHTLSTYPELNSSIKmEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIKHmEIDIIKRETTGTGPNVYHENDTIAKYEImDGAPVRGESIPIRLFLAGYELTPTmRDINKKFSVRYYLNLVLIDEEERRYFKQQEVVLWRKG 296
                                    18        28        38        48        58        68        78        88        98       108       118       128       138      |148       158     | 168       178       188       198      |208       218       228     | 238       248       258|      268       278       288        
                                                                                                                                                                  145-MSE            164-MSE                                  205-MSE                      234-MSE                  259-MSE                                 

   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  (0, 0)

(no "SCOP Domain" information available for 2R51)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R51)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (VP26B_MOUSE | Q8C0E2)
molecular function
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    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: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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030904    retromer complex    A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VP26B_MOUSE | Q8C0E23lh8 3lh9 3lha

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