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(-) Description

Title :  THE IDAS:GEMININ HETERODIMERIC PARALLEL COILED-COIL
 
Authors :  C. Caillat, A. Perrakis
Date :  06 Jun 13  (Deposition) - 02 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Cycle, Dna Replication Licensing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Caillate, E. D. Pefani, P. J. Gillespie, S. Taraviras, J. J. Blow, Z. Lygerou, A. Perrakis
The Geminin And Idas Coiled Coils Preferentially Form A Heterodimer That Inhibits Geminin Function In Dna Replication Licensing
J. Biol. Chem. V. 288 31624 2013
PubMed-ID: 24064211  |  Reference-DOI: 10.1074/JBC.M113.491928

(-) Compounds

Molecule 1 - GEMININ
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-NKI-LIC
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentCOILED-COIL, RESIDUES 83-160
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - MULTICILIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET-22B
    Expression System Vector TypePLASMID
    FragmentCOILED-COIL, RESIDUES 173-245
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMULTICILIATE DIFFERENTIATION AND DNA SYNTHESIS-ASSOCIATED CELL CYCLE PROTEIN, PROTEIN IDAS, IDAS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PG42Ligand/IonTETRAETHYLENE GLYCOL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:127 , GLN B:211BINDING SITE FOR RESIDUE PG4 A1161
2AC2SOFTWARELYS A:108 , PRO B:176BINDING SITE FOR RESIDUE PG4 A1162
3AC3SOFTWAREALA A:103 , GLU A:104 , ARG A:107 , TRP B:182 , VAL B:185 , ASN B:189BINDING SITE FOR RESIDUE PO4 A1163
4AC4SOFTWARELYS A:105 , ARG A:106 , GLU A:116BINDING SITE FOR RESIDUE PO4 A1164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BRY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BRY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BRY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BRY)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003565091aENSE00001917299chr6:24775159-24775340182GEMI_HUMAN-00--
1.3bENST000003565093bENSE00000848247chr6:24777450-2477752576GEMI_HUMAN1-17170--
1.4ENST000003565094ENSE00000693554chr6:24780891-2478096878GEMI_HUMAN18-43260--
1.5bENST000003565095bENSE00000693556chr6:24781705-24781849145GEMI_HUMAN44-92491A:92-921
1.6bENST000003565096bENSE00000693558chr6:24784315-2478439783GEMI_HUMAN92-119281A:92-11928
1.7ENST000003565097ENSE00000693560chr6:24784672-24784782111GEMI_HUMAN120-156371A:120-15637
1.8bENST000003565098bENSE00001419614chr6:24785866-24786323458GEMI_HUMAN157-209531A:157-1604

(-) 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:69
 aligned with GEMI_HUMAN | O75496 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:69
                                   101       111       121       131       141       151         
           GEMI_HUMAN    92 ENPSSQYWKEVAEKRRKALYEALKENEKLHKEIEQKDNEIARLKKENKELAEVAEHVQYMAELIERLNG 160
               SCOP domains d4brya_ A: automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1---------------------------Exon 1.7  PDB: A:120-156             1.8b Transcript 1 (1)
           Transcript 1 (2) Exon 1.6b  PDB: A:92-119    ----------------------------------------- Transcript 1 (2)
                 4bry A  92 ENPSSQYWKEVAEKRRKALYEALKENEKLHKEIEQKDNEIARLKKENKELAEVAEHVQYMAELIERLNG 160
                                   101       111       121       131       141       151         

Chain B from PDB  Type:PROTEIN  Length:69
 aligned with MCIN_HUMAN | D6RGH6 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:69
                                   185       195       205       215       225       235         
           MCIN_HUMAN   176 PPPEQYWKEVADQNQRALGDALVENNQLHVTLTQKQEEIASLKERNVQLKELASRTRHLASVLDKLMIT 244
               SCOP domains d4bryb_ B: automated matches                                          SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 4bry B 176 PPPEQYWKEVADQNQRALGDALVENNQLHVTLTQKQEEIASLKERNVQLKELASRTRHLASVLDKLMIT 244
                                   185       195       205       215       225       235         

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BRY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BRY)

(-) Gene Ontology  (26, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GEMI_HUMAN | O75496)
molecular function
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    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:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

Chain B   (MCIN_HUMAN | D6RGH6)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
    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:0030030    cell projection organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0098534    centriole assembly    A cellular process that results in the assembly of one or more centrioles.
    GO:0044458    motile cilium assembly    The aggregation, arrangement and bonding together of a set of components to form a motile cilium.
    GO:1903251    multi-ciliated epithelial cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a multi-ciliated epithelial cell.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GEMI_HUMAN | O754961t6f 1uii 2lp0 2wvr

(-) Related Entries Specified in the PDB File

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