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(-) Description

Title :  CRYSTAL STRUCTURE OF WD40 REPEATS PROTEIN WDR92
 
Authors :  M. F. Amaya, Z. Li, H. He, A. Seitova, S. Ni, A. M. Edwards, C. H. Arrowsmit J. Weigelt, C. Bountra, A. Bochkarev, J. Min, H. Ouyang, Structural G Consortium (Sgc)
Date :  29 Jun 09  (Deposition) - 18 Aug 09  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Wd40 Repeats, Wdr92, Structural Genomics, Structural Genomics Consortium, Sgc, Apoptosis, Wd Repeat, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Xu, J. Min
Structure And Function Of Wd40 Domain Proteins.
Protein Cell V. 2 202 2011
PubMed-ID: 21468892  |  Reference-DOI: 10.1007/S13238-011-1018-1

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 92
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneWDR92
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymWD REPEAT-CONTAINING PROTEIN MONAD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3I2N)

(-) Sites  (0, 0)

(no "Site" information available for 3I2N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I2N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I2N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053438M241VWDR92_HUMANPolymorphism13009282AM241V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I2N)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002951211aENSE00001738493chr2:68384692-68384393300WDR92_HUMAN1-61611A:5-61 (gaps)57
1.2ENST000002951212ENSE00002057213chr2:68374699-68374599101WDR92_HUMAN62-95341A:62-9534
1.3ENST000002951213ENSE00002052490chr2:68371847-68371717131WDR92_HUMAN95-139451A:95-13945
1.4ENST000002951214ENSE00002058429chr2:68368927-68368826102WDR92_HUMAN139-173351A:139-17335
1.5aENST000002951215aENSE00002057114chr2:68365989-68365874116WDR92_HUMAN173-211391A:173-21139
1.6ENST000002951216ENSE00002054305chr2:68364565-68364431135WDR92_HUMAN212-256451A:212-25645
1.7aENST000002951217aENSE00002032224chr2:68361931-6836183498WDR92_HUMAN257-289331A:257-28933
1.9bENST000002951219bENSE00001604920chr2:68358577-683569351643WDR92_HUMAN289-357691A:289-353 (gaps)65

(-) 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:345
 aligned with WDR92_HUMAN | Q96MX6 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:349
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344         
          WDR92_HUMAN     5 EKPQIIAHIQKGFNYTVFDCKWVPCSAKFVTMGNFARGTGVIQLYEIQHGDLKLLREIEKAKPIKCGTFGATSLQQRYLATGDFGGNLHIWNLEAPEMPVYSVKGHKEIINAIDGIGGLGIGEGAPEIVTGSRDGTVKVWDPRQKDDPVANMEPVQGENKRDCWTVAFGNAYNQEERVVCAGYDNGDIKLFDLRNMALRWETNIKNGVCSLEFDRKDISMNKLVATSLEGKFHVFDMRTQHPTKGFASVSEKAHKSTVWQVRHLPQNRELFLTAGGAGGLHLWKYEYPIQRSKKDSEGIEMGVAGSVSLLQNVTLSTQPISSLDWSPDKRGLCVCSSFDQTVRVLIVTK 353
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee...eeeeeee.....eeeeeee--...eeeeeeee....eeeeeeeee...eeeee..........eeeee....eeee.........eee......eeeeeeehhhhh.....eeeeee....eeee.........eee..........eeeeeee........eeeeee...eeeeee....eeeeeee....eeeeee........eeeeee...eeeeee...........eeeee.....eeeeeee..eeeeeeeee...eeeeeeee.....--............eeeeeeeee.....eeeeee......eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:5-61 (gaps) UniProt: 1-61 [INCOMPLETE] Exon 1.2  PDB: A:62-95            -------------------------------------------Exon 1.4  PDB: A:139-173           --------------------------------------Exon 1.6  PDB: A:212-256 UniProt: 212-256    Exon 1.7a  PDB: A:257-289        ---------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.3  PDB: A:95-139 UniProt: 95-139      ---------------------------------Exon 1.5a  PDB: A:173-211              -----------------------------------------------------------------------------Exon 1.9b  PDB: A:289-353 (gaps) UniProt: 289-357 [INCOMPLETE]    Transcript 1 (2)
                 3i2n A   5 EKPQIIAHIQKGFNYTVFDCKWVPCSAKFVTMGN--RGTGVIQLYEIQHGDLKLLREIEKAKPIKCGTFGATSLQQRYLATGDFGGNLHIWNLEAPEMPVYSVKGHKEIINAIDGIGGLGIGEGAPEIVTGSRDGTVKVWDPRQKDDPVANMEPVQGENKRDCWTVAFGNAYNQEERVVCAGYDNGDIKLFDLRNMALRWETNIKNGVCSLEFDRKDISMNKLVATSLEGKFHVFDMRTQHPTKGFASVSEKAHKSTVWQVRHLPQNRELFLTAGGAGGLHLWKYEYPIQR--KDSEGIEMGVAGSVSLLQNVTLSTQPISSLDWSPDKRGLCVCSSFDQTVRVLIVTK 353
                                    14        24        34   |  | 44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294|  |   304       314       324       334       344         
                                                            38 41                                                                                                                                                                                                                                                           295  |                                                       
                                                                                                                                                                                                                                                                                                                               298                                                       

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  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 3I2N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I2N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I2N)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (WDR92_HUMAN | Q96MX6)
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:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.

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