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(-) Description

Title :  MAMMALIAN SCAN DOMAIN DIMER IS A DOMAIN-SWAPPED HOMOLOGUE OF THE HIV CAPSID C-TERMINAL DOMAIN
 
Authors :  D. Ivanov, J. R. Stone, J. L. Maki, T. Collins, G. Wagner
Date :  09 Dec 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Scan Domain; Retroviral Capsid C-Terminal Domain; Dimer; C2H2 Zinc Finger Associated, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Ivanov, J. R. Stone, J. L. Maki, T. Collins, G. Wagner
Mammalian Scan Domain Dimer Is A Domain-Swapped Homolog Of The Hiv Capsid C-Terminal Domain
Mol. Cell V. 17 137 2005
PubMed-ID: 15629724  |  Reference-DOI: 10.1016/J.MOLCEL.2004.12.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 174
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSCAN DOMAIN, RESIDUES 37-132
    GeneZNF174, ZSCAN8
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAW-1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Y7Q)

(-) Sites  (0, 0)

(no "Site" information available for 1Y7Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y7Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y7Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y7Q)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SCAN_BOXPS50804 SCAN box profile.ZN174_HUMAN46-126
 
  2A:46-126
B:46-126

(-) Exons   (1, 2)

NMR Structure (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002686551bENSE00001838202chr16:3451420-3452406987ZN174_HUMAN1-1341342A:35-132 (gaps)
B:35-132 (gaps)
101
101
1.2ENST000002686552ENSE00000666898chr16:3454426-3454648223ZN174_HUMAN135-209750--
1.4ENST000002686554ENSE00000666899chr16:3458321-34593701050ZN174_HUMAN209-4071990--

(-) Sequences/Alignments

NMR Structure
   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:98
 aligned with ZN174_HUMAN | Q15697 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:101
                                    41        51        61        71        81        91       101       111       121       131 
          ZN174_HUMAN    32 GPPLQKNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPPEIQARVRHRCPMSSKEIVTLVEDFHRASKKPK 132
               SCOP domains -----d1y7qa1 A:37-132 Zinc finger protein 174                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---......hhhhhhhhh........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SCAN_BOX  PDB: A:46-126 UniProt: 46-126                                          ------ PROSITE
               Transcript 1 Exon 1.1b  PDB: A:35-132 (gaps) UniProt: 1-134 [INCOMPLETE]                                           Transcript 1
                 1y7q A  35 GS---KNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDFHRASKKPK 132
                             |   |  41        51        61        71        81        91       101       111       121       131 
                             |  37                                                                                               
                            36                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with ZN174_HUMAN | Q15697 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:101
                                    41        51        61        71        81        91       101       111       121       131 
          ZN174_HUMAN    32 GPPLQKNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPPEIQARVRHRCPMSSKEIVTLVEDFHRASKKPK 132
               SCOP domains d1   y7qb_ B: Zinc finger protein 174                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------SCAN-1y7qB01 B:40-132                                                                         Pfam domains (1)
           Pfam domains (2) --------SCAN-1y7qB02 B:40-132                                                                         Pfam domains (2)
         Sec.struct. author ..---......hhhhhhhh..........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SCAN_BOX  PDB: B:46-126 UniProt: 46-126                                          ------ PROSITE
               Transcript 1 Exon 1.1b  PDB: B:35-132 (gaps) UniProt: 1-134 [INCOMPLETE]                                           Transcript 1
                 1y7q B  35 GS---KNCPDPELCRQSFRRFCYQEVSGPQEALSQLRQLCRQWLQPELHTKEQILELLVMEQFLTILPEEIQARVRHRCLMSSKEIVTLVEDFHRASKKPK 132
                             |   |  41        51        61        71        81        91       101       111       121       131 
                            36  37                                                                                               

   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y7Q)

(-) Pfam Domains  (1, 2)

NMR Structure

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A,B   (ZN174_HUMAN | Q15697)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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: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:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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