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(-) Description

Title :  CRYSTAL STRUCTURE OF SPINDLIN1
 
Authors :  Q. Zhao, L. Qin, F. Jiang, B. Wu, W. Yue, F. Xu, Z. Rong, H. Yuan, X. Xie, Y. Gao, C. Bai, M. Bartlam
Date :  02 Nov 06  (Deposition) - 28 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Repeat Domains, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Zhao, L. Qin, F. Jiang, B. Wu, W. Yue, F. Xu, Z. Rong, H. Yuan, X. Xie, Y. Gao, C. Bai, M. Bartlam, X. Pei, Z. Rao
Structure Of Human Spindlin1. Tandem Tudor-Like Domains For Cell Cycle Regulation
J. Biol. Chem. V. 282 647 2007
PubMed-ID: 17082182  |  Reference-DOI: 10.1074/JBC.M604029200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPINDLIN-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-237 (26-262)
    GeneSPIN, OCR, SPIN1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOVARIAN CANCER-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:92 , VAL A:93 , ALA A:94 , THR A:95 , MET A:137 , ASN A:138 , THR A:139 , TRP A:140 , HOH A:336BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREARG A:97 , ILE A:98 , ARG A:133 , ASN A:138 , HOH A:306 , HOH A:380BINDING SITE FOR RESIDUE PO4 A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NS2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NS2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053690A221PSPIN1_HUMANPolymorphism34794905A/BA196P

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NS2)

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003758591aENSE00001089382chr9:91003334-91003453120SPIN1_HUMAN-00--
1.6ENST000003758596ENSE00002152660chr9:91041297-91041506210SPIN1_HUMAN1-18180--
1.7ENST000003758597ENSE00001468610chr9:91063856-9106390449SPIN1_HUMAN18-34170--
1.8cENST000003758598cENSE00000817830chr9:91077411-91077664254SPIN1_HUMAN34-119862A:25-94
B:27-91
70
65
1.9bENST000003758599bENSE00000710811chr9:91083287-91083520234SPIN1_HUMAN119-197792A:94-170
B:104-168 (gaps)
77
65
1.10cENST0000037585910cENSE00001468598chr9:91089993-910936093617SPIN1_HUMAN197-262662A:181-235
B:184-234
55
51

(-) 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:201
 aligned with SPIN1_HUMAN | Q9Y657 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:211
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 
          SPIN1_HUMAN    50 RRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVK 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......eeeeeeeeee.......eeeee......eee.......eeeeeee..........hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee..eeeeeeehhhhhhhh..eeee..----------...........eeeee.....eeeeeeeee......eeeeee......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------P--------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8c  PDB: A:25-94 UniProt: 34-119 [INCOMPLETE]                  -----------------------------------------------------------------------------Exon 1.10c  PDB: A:181-235 UniProt: 197-262 [INCOMPLETE]         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.9b  PDB: A:94-170 UniProt: 119-197 [INCOMPLETE]                         --------------------------------------------------------------- Transcript 1 (2)
                 2ns2 A  25 RRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPD----------PGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVK 235
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164     |   -      |184       194       204       214       224       234 
                                                                                                                                                                           170        181                                                      

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with SPIN1_HUMAN | Q9Y657 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:208
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        
          SPIN1_HUMAN    52 NIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Spin-Ssty-2ns2B01 B:189-234                    Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Spin-Ssty-2ns2B02 B:189-234                    Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Spin-Ssty-2ns2B03 B:189-234                    Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Spin-Ssty-2ns2B04 B:189-234                    Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Spin-Ssty-2ns2B05 B:189-234                    Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Spin-Ssty-2ns2B06 B:189-234                    Pfam domains (6)
         Sec.struct. author .....eeeeee......eeeeeeeeeee.......eeeee......eee.......eeeeee...------------.......eeee.---------.eeeeeeee.......eeeee..eeeeeee.hhhhhhh......---------------........eeeee.....eeeeeeeee......eeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------P-------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8c  PDB: B:27-91 UniProt: 34-119 [INCOMPLETE]                -----------------------------------------------------------------------------Exon 1.10c  PDB: B:184-234 UniProt: 197-262 [INCOMPLETE]        Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.9b  PDB: B:104-168 (gaps) UniProt: 119-197 [INCOMPLETE]                 -------------------------------------------------------------- Transcript 1 (2)
                 2ns2 B  27 NIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPD------------ADTMIGKAVEHM---------EWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIM---------------VVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 234
                                    36        46        56        66        76        86    |    -       106        |-       126       136       146       156       166 |       -       186       196       206       216       226        
                                                                                           91          104        115       125                                        168             184                                                  

   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 2NS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NS2)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPIN1_HUMAN | Q9Y657)
molecular function
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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: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: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:0007276    gamete generation    The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    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:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    GO:0009303    rRNA transcription    The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
cellular component
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIN1_HUMAN | Q9Y6574h75 4mzf 4mzg 4mzh 5jsg 5jsj

(-) Related Entries Specified in the PDB File

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