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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN VPS26
 
Authors :  H. Shi, R. Rojas, J. S. Bonifacino, J. H. Hurley
Date :  08 Dec 05  (Deposition) - 30 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Arrestin, Retromer, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Shi, R. Rojas, J. S. Bonifacino, J. H. Hurley
The Retromer Subunit Vps26 Has An Arrestin Fold And Binds Vps35 Through Its C-Terminal Domain.
Nat. Struct. Mol. Biol. V. 13 540 2006
PubMed-ID: 16732284  |  Reference-DOI: 10.1038/NSMB1103

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING 26
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMR101
    Expression System StrainBL21 (DE3) GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneVPS26A, VPS26
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVESICLE PROTEIN SORTING 26, HVPS26

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CAF2Mod. Amino AcidS-DIMETHYLARSINOYL-CYSTEINE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:39 , TYR A:40 , TYR A:147 , ASP A:148BINDING SITE FOR RESIDUE GOL A 340

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003733821ENSE00001460473chr10:70883268-7088330235VP26A_HUMAN-00--
1.2aENST000003733822aENSE00001460472chr10:70883416-70884036621VP26A_HUMAN1-110--
1.3ENST000003733823ENSE00001095997chr10:70892654-70892803150VP26A_HUMAN2-51501A:6-5146
1.4ENST000003733824ENSE00000933686chr10:70915568-7091564376VP26A_HUMAN52-77261A:52-7726
1.5ENST000003733825ENSE00000933687chr10:70916763-70916919157VP26A_HUMAN77-129531A:77-12953
1.6bENST000003733826bENSE00001278296chr10:70917803-70917967165VP26A_HUMAN129-184561A:129-18456
1.7ENST000003733827ENSE00000933689chr10:70922162-70922268107VP26A_HUMAN184-220371A:184-22037
1.8ENST000003733828ENSE00001278281chr10:70925798-7092586669VP26A_HUMAN220-243241A:220-23819
1.9cENST000003733829cENSE00000933691chr10:70928245-70928387143VP26A_HUMAN243-290481A:245-29046
1.11eENST0000037338211eENSE00001460424chr10:70930912-709326171706VP26A_HUMAN291-327371A:291-2999

(-) 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:288
 aligned with VP26A_HUMAN | O75436 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:294
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    
          VP26A_HUMAN     6 GFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAP 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee.hhhhh.eeeee.....eeeeeee.....eeeeeeeee......eee..eeeeeeeeeee......eeeeeeeeeeee..eee...eeeeeee.........ee...eeeeeeeeeee......eeeeeeeee............eeeeeee...eeeeeee...eee...eeeeeeeeeee...eeeeeeeeeeeeee.hhhhheeeeeeeeeee....------.eeeeee.........eeeee..eeeeeeeeeeeee....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:6-51 UniProt: 2-51           Exon 1.4  PDB: A:52-77    ---------------------------------------------------Exon 1.6b  PDB: A:129-184 UniProt: 129-184              -----------------------------------Exon 1.8  PDB: A:220-238-----------------------------------------------1.11e     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------Exon 1.5  PDB: A:77-129 UniProt: 77-129              ------------------------------------------------------Exon 1.7  PDB: A:184-220             ----------------------Exon 1.9c  PDB: A:245-290 UniProt: 243-290      --------- Transcript 1 (2)
                 2fau A   6 GFFGPIcEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDcLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDG------SIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAP 299
                                  | 15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  |    245       255       265       275       285       295    
                                 12-CAF                                                                                                                                                          173-CAF                                                          238    245                                                      

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  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 2FAU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FAU)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VP26A_HUMAN | O75436)
molecular function
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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:0016241    regulation of macroautophagy    Any process that modulates the frequency, rate or extent of macroautophagy.
    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:1990126    retrograde transport, endosome to plasma membrane    The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins.
    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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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.
    GO:0030906    retromer, cargo-selective complex    The trimeric subcomplex of the retromer, believed to be closely associated with the membrane. This trimeric complex is responsible for recognizing and binding to cargo molecules. The complex comprises three Vps proteins in both yeast and mammalian cells: Vps35p, Vps29p, and Vps26p in yeast, and VPS35, VPS29 and VPS26A or VPS26B in mammals.
    GO:0097422    tubular endosome    A network of fine tubules in the vicinity of the Golgi complex and around the centriole.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VP26A_HUMAN | O754365f0j 5f0l 5f0m 5f0p

(-) Related Entries Specified in the PDB File

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