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(-) Description

Title :  SOLUTION STRUCTURE OF THE ZF-B_BOX TYPE2 DOMAIN OF HUMAN TRIPARTITE MOTIF PROTEIN TRIM29 ISOFORM ALPHA
 
Authors :  K. Inoue, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 May 05  (Deposition) - 23 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zf-B_box Domain, Tripartite Motif Protein 29, Trim29, Ataxia-Telangiectasia Group D-Associated Protein, Atdc, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Inoue, F. Hayashi, S. Yokoyama
Solution Structure Of The Zf-B_box Type2 Domain Of Human Tripartite Motif Protein Trim29 Isoform Alpha
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIPARTITE MOTIF PROTEIN 29
    ChainsA
    EngineeredYES
    Expression System PlasmidP040906-08
    Expression System Vector TypePLASMID
    FragmentZF-B_BOX DOMAIN
    GeneTRIM29, ATDC
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymATAXIA-TELANGIECTASIA GROUP D-ASSOCIATED PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:21 , HIS A:24 , CYS A:40 , CYS A:43BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARECYS A:32 , ASP A:35 , HIS A:48 , HIS A:51BINDING SITE FOR RESIDUE ZN A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_BBOXPS50119 Zinc finger B-box type profile.TRI29_HUMAN220-260  1A:16-56

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4bENST000003418464bENSE00002190568chr11:120009161-1200079361226TRI29_HUMAN1-2682681A:1-64 (gaps)105
1.5cENST000003418465cENSE00001329495chr11:119999203-11999910896TRI29_HUMAN269-300321A:65-728
1.6bENST000003418466bENSE00000990447chr11:119998277-119998044234TRI29_HUMAN301-378780--
1.7bENST000003418467bENSE00000990448chr11:119996597-119996399199TRI29_HUMAN379-445670--
1.11aENST0000034184611aENSE00000990449chr11:119993763-119993662102TRI29_HUMAN445-479350--
1.14ENST0000034184614ENSE00001315675chr11:119991373-11999128193TRI29_HUMAN479-510320--
1.16ENST0000034184616ENSE00001295962chr11:119989029-11998893199TRI29_HUMAN510-543340--
1.17fENST0000034184617fENSE00000990453chr11:119986122-11998604677TRI29_HUMAN543-568260--
1.19bENST0000034184619bENSE00001372895chr11:119983184-1199819831202TRI29_HUMAN569-588200--

(-) 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:72
 aligned with TRI29_HUMAN | Q14134 from UniProtKB/Swiss-Prot  Length:588

    Alignment length:113
                                   173       183       193       203       213       223       233       243       253       263       273   
          TRI29_HUMAN   164 SKSGSEEVLCDSCIGNKQKAVKSCLVCQASFCELHLKPHLEGAAFRDHQLLEPIRDFEARKCPVHGKTMELFCQTDQTCICYLCMFQEHKNHSTVTVEEAKAEKETELSLQKE 276
               SCOP domains ------------------------------------------------d2csva1 A:8-66 Tripartite motif-containing protein 29      ------ SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......--------.---------------------------------......................eee.....eehhhhhhh......eeehhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------ZF_BBOX  PDB: A:16-56 UniProt: 220-260   ---------------- PROSITE
               Transcript 1 Exon 1.4b  PDB: A:1-64 (gaps) UniProt: 1-268 [INCOMPLETE]                                                1.5c     Transcript 1
                 2csv A   1 GSSGSS--------G---------------------------------QLLEPIRDFEARKCPVHGKTMELFCQTDQTCICYLCMFQEHKNHSTVTVEEAKAEKETESGPSSG  72
                                 |   -    |    -         -         -        |9        19        29        39        49        59        69   
                                 6        7                                 8                                                                

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (TRI29_HUMAN | Q14134)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of 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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:1900181    negative regulation of protein localization to nucleus    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus.
    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:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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