Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE B2 BOX FROM MURF1 IN DIMERIC STATE
 
Authors :  O. Mayans, M. Mrosek
Date :  06 Jun 08  (Deposition) - 07 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Zinc-Binding Motif, Ring-Like Fold, Coiled Coil, Cytoplasm, Ligase, Metal-Binding, Muscle Protein, Nucleus, Polymorphism, Ubl Conjugation Pathway, Zinc, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Mrosek, S. Meier, Z. Ucurum-Fotiadis, E. Von Castelmur, E. Hedbom, A. Lustig, S. Grzesiek, D. Labeit, S. Labeit, O. Mayans
Structural Analysis Of B-Box 2 From Murf1: Identification Of A Novel Self-Association Pattern In A Ring-Like Fold
Biochemistry V. 47 10722 2008
PubMed-ID: 18795805  |  Reference-DOI: 10.1021/BI800733Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE TRIM63
    ChainsA, B, C
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM-11
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentB2-BOX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRIPARTITE MOTIF-CONTAINING PROTEIN 63, MUSCLE- SPECIFIC RING FINGER PROTEIN 1, MURF1, MURF-1, RING FINGER PROTEIN 28, STRIATED MUSCLE RING ZINC FINGER PROTEIN, IRIS RING FINGER PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)AB 
Biological Unit 2 (2x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:6 , HIS A:9 , CYS A:26 , CYS A:29BINDING SITE FOR RESIDUE ZN A 46
2AC2SOFTWARECYS A:18 , CYS A:21 , HIS A:35 , CYS A:38BINDING SITE FOR RESIDUE ZN A 47
3AC3SOFTWARECYS B:6 , HIS B:9 , CYS B:26 , CYS B:29BINDING SITE FOR RESIDUE ZN B 46
4AC4SOFTWARECYS B:18 , CYS B:21 , HIS B:35 , CYS B:38BINDING SITE FOR RESIDUE ZN B 47
5AC5SOFTWARECYS C:18 , CYS C:21 , HIS C:35 , CYS C:38BINDING SITE FOR RESIDUE ZN C 46
6AC6SOFTWARECYS C:6 , HIS C:9 , CYS C:26 , CYS C:29BINDING SITE FOR RESIDUE ZN C 47

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DDT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DDT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_074098E126DTRI63_HUMANPolymorphism142601731A/B/CE10D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_074098E126DTRI63_HUMANPolymorphism142601731A/BE10D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_074098E126DTRI63_HUMANPolymorphism142601731CE10D

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_BBOXPS50119 Zinc finger B-box type profile.TRI63_HUMAN117-159
 
 
  3A:1-43
B:1-43
C:1-43
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_BBOXPS50119 Zinc finger B-box type profile.TRI63_HUMAN117-159
 
 
  2A:1-43
B:1-43
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_BBOXPS50119 Zinc finger B-box type profile.TRI63_HUMAN117-159
 
 
  2-
-
C:1-43

(-) Exons   (2, 5)

Asymmetric Unit (2, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003742721bENSE00001462989chr1:26394124-26393827298TRI63_HUMAN1-53530--
1.2ENST000003742722ENSE00001036617chr1:26392931-26392759173TRI63_HUMAN54-111582A:-2-0 (gaps)
B:-2-0 (gaps)
-
6
6
-
1.3bENST000003742723bENSE00001036615chr1:26387825-26387657169TRI63_HUMAN111-167573A:1-45
B:1-44
C:1-44
45
44
44
1.4ENST000003742724ENSE00001036596chr1:26386852-2638675796TRI63_HUMAN168-199320--
1.5ENST000003742725ENSE00001036620chr1:26385114-26384881234TRI63_HUMAN200-277780--
1.6ENST000003742726ENSE00001036623chr1:26384141-2638411923TRI63_HUMAN278-28580--
1.7ENST000003742727ENSE00001036610chr1:26383818-26383694125TRI63_HUMAN285-327430--
1.8ENST000003742728ENSE00001154105chr1:26380455-2638038472TRI63_HUMAN327-351250--
1.9ENST000003742729ENSE00001462984chr1:26378374-26377795580TRI63_HUMAN351-35330--

(-) Sequences/Alignments

Asymmetric 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:48
 aligned with TRI63_HUMAN | Q969Q1 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:99
                                    72        82        92       102       112       122       132       142       152         
          TRI63_HUMAN    63 GSSVSMSGGRFRCPTCRHEVIMDRHGVYGLQRNLLVENIIDIYKQECSSRPLQKGSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQS 161
               SCOP domains d   3d                                                dta_ A: automated matches                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---..------------------------------------------------...............eee....eeehhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------D----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------ZF_BBOX  PDB: A:1-43 UniProt: 117-159      -- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:-2-0 (gaps) UniProt: 54-111     -------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3b  PDB: A:1-45 UniProt: 111-167             Transcript 1 (2)
                 3ddt A  -2 G---AM------------------------------------------------GSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQS  45
                            |   ||   -         -         -         -         -    |    6        16        26        36         
                            |  -1|                                                1                                            
                           -2    0                                                                                             

Chain B from PDB  Type:PROTEIN  Length:47
 aligned with TRI63_HUMAN | Q969Q1 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:98
                                    72        82        92       102       112       122       132       142       152        
          TRI63_HUMAN    63 GSSVSMSGGRFRCPTCRHEVIMDRHGVYGLQRNLLVENIIDIYKQECSSRPLQKGSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQ 160
               SCOP domains d   3d                                                dtb_ B: automated matches                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---..------------------------------------------------...............eee....eeehhhhhhh.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------D---------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------ZF_BBOX  PDB: B:1-43 UniProt: 117-159      - PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:-2-0 (gaps) UniProt: 54-111     ------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3b  PDB: B:1-44 UniProt: 111-167            Transcript 1 (2)
                 3ddt B  -2 G---AM------------------------------------------------GSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQ  44
                            |   ||   -         -         -         -         -    |    6        16        26        36        
                           -2  -1|                                                1                                           
                                 0                                                                                            

Chain C from PDB  Type:PROTEIN  Length:44
 aligned with TRI63_HUMAN | Q969Q1 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:44
                                   126       136       146       156    
          TRI63_HUMAN   117 GSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQ 160
               SCOP domains d3ddtc_ C: automated matches                 SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ...............eee....eeehhhhhhh.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------D---------------------------------- SAPs(SNPs)
                    PROSITE ZF_BBOX  PDB: C:1-43 UniProt: 117-159      - PROSITE
           Transcript 1 (1) -------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.3b  PDB: C:1-44 UniProt: 111-167      Transcript 1 (2)
                 3ddt C   1 GSHPMCKEHEDEKINIYCLTCEVPTCSMCKVFGIHKACEVAPLQ  44
                                    10        20        30        40    

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DDT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DDT)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (TRI63_HUMAN | Q969Q1)
molecular function
    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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0031432    titin binding    Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively.
    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:0006936    muscle contraction    A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0014878    response to electrical stimulus involved in regulation of muscle adaptation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. This process occurs as part of the regulation of muscle adaptation.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0014732    skeletal muscle atrophy    A process, occurring in skeletal muscle, that is characterized by a decrease in protein content, fiber diameter, force production and fatigue resistance in response to different conditions such as starvation, aging and disuse.
cellular component
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0043292    contractile fiber    Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ddt)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ddt
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TRI63_HUMAN | Q969Q1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TRI63_HUMAN | Q969Q1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TRI63_HUMAN | Q969Q12d8u 4m3l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DDT)