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(-) Description

Title :  SOLUTION STRUCTURE OF THE ZINC FINGER, C3HC4 TYPE (RING FINGER) DOMAIN OF TRIPARTITE MOTIF-CONTAINING PROTEIN 5
 
Authors :  H. Abe, K. Miyamoto, N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Feb 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Metal Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Abe, K. Miyamoto, N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of The Zinc Finger, C3Hc4 Type (Ring Finger) Domain Of Tripartite Motif-Containing Protein 5
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIPARTITE MOTIF-CONTAINING PROTEIN 5
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression System PlasmidP060411-09
    Expression System Vector TypePLASMID
    FragmentZINC FINGER, C3HC4 TYPE (RING FINGER)
    GeneTRIM5, RNF88
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymRING FINGER PROTEIN 88

 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:22 , CYS A:25 , CYS A:42 , CYS A:45BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:37 , HIS A:39 , CYS A:62 , CYS A:65BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

NMR Structure (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_060707G31STRIM5_HUMANPolymorphism59896509AG38S
2UniProtVAR_017397H43YTRIM5_HUMANPolymorphism3740996AH50Y
3UniProtVAR_060708C58YTRIM5_HUMANPolymorphism61432120AC65Y

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_2PS50089 Zinc finger RING-type profile.TRIM5_HUMAN15-59  1A:22-66
2ZF_RING_1PS00518 Zinc finger RING-type signature.TRIM5_HUMAN30-39  1A:37-46

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6bENST000003800346bENSE00001342726chr11:5706293-5706098196TRIM5_HUMAN-00--
1.8bENST000003800348bENSE00000903262chr11:5701468-5700991478TRIM5_HUMAN1-1391391A:8-8578
1.9aENST000003800349aENSE00001702391chr11:5700399-570030496TRIM5_HUMAN140-171320--
1.10bENST0000038003410bENSE00001483548chr11:5699664-5699434231TRIM5_HUMAN172-248770--
1.11ENST0000038003411ENSE00001483528chr11:5688941-568891923TRIM5_HUMAN249-25680--
1.13bENST0000038003413bENSE00001762427chr11:5687311-5687211101TRIM5_HUMAN256-290350--
1.14aENST0000038003414aENSE00001624747chr11:5686912-568688627TRIM5_HUMAN290-299100--
1.14hENST0000038003414hENSE00001811417chr11:5686625-56847871839TRIM5_HUMAN299-4931950--

(-) 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:85
 aligned with TRIM5_HUMAN | Q9C035 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:85
                                   1                                                                             
                                   | 3        13        23        33        43        53        63        73     
           TRIM5_HUMAN    - -------MASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHVANIVE 78
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................................hhhhhhhhhh................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------S-----------Y--------------Y-------------------- SAPs(SNPs)
                PROSITE (1) ---------------------ZF_RING_2  PDB: A:22-66 UniProt: 15-59       ------------------- PROSITE (1)
                PROSITE (2) ------------------------------------ZF_RING_1 --------------------------------------- PROSITE (2)
               Transcript 1 -------Exon 1.8b  PDB: A:8-85 UniProt: 1-139 [INCOMPLETE]                             Transcript 1
                  2ecv A  1 GSSGSSGMASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHVANIVE 85
                                    10        20        30        40        50        60        70        80     

   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 2ECV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 35)

NMR Structure(hide GO term definitions)
Chain A   (TRIM5_HUMAN | Q9C035)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0008329    signaling pattern recognition receptor activity    Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species, or damage-associated molecular pattern (DAMP), an endogenous molecule released from damaged cells), and transmitting a signal to initiate a change in cell activity.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0002218    activation of innate immune response    Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0046597    negative regulation of viral entry into host cell    Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell.
    GO:1902187    negative regulation of viral release from host cell    Any process that stops, prevents or reduces the frequency, rate or extent of viral release from host cell.
    GO:0002221    pattern recognition receptor signaling pathway    Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0070206    protein trimerization    The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0031664    regulation of lipopolysaccharide-mediated signaling pathway    Any process that modulates the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    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: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: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:1990462    omegasome    Omega-shaped (as in the Greek capital letter) intracellular membrane-bounded organelle enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. Omegasomes are the first step of the formation of autophagosomes via the pre-autophagosomal structures.

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        TRIM5_HUMAN | Q9C0352yrg

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