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

(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF A RNA-POLYMERASE II BINDING PROTEIN WITH ASSOCIATED LIGAND.
 
Authors :  T. Kamenski, S. Heilmeier, T. Meinhart, P. Cramer
Date :  19 May 04  (Deposition) - 31 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Kamenski, S. Heilmeier, T. Meinhart, P. Cramer
Structure And Mechanism Of Rna Polymerase Ii Ctd Phosphatases.
Mol. Cell V. 15 399 2004
PubMed-ID: 15304220  |  Reference-DOI: 10.1016/J.MOLCEL.2004.06.035
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXY-TERMINAL DOMAIN RNA POLYMERASE II POLYPEPTIDE A SMALL PHOSPHATASE 1
    ChainsA
    EC Number3.1.3.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCTDSP1, NIF3, NLIIF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR LIM INTERACTOR-INTERACTING FACTOR 3, NLI- INTERACTING FACTOR 3, NLI-IF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1BFD1Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
2CIT1Ligand/IonCITRIC ACID
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREBFD A:96 , ASP A:98 , ASN A:207 , HOH A:290 , HOH A:380BINDING SITE FOR RESIDUE MG A 273
2AC2SOFTWARESER A:105 , PHE A:106 , ILE A:120 , TYR A:158 , HOH A:329 , HOH A:374BINDING SITE FOR RESIDUE CIT A 274

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TA0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TA0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TA0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FCP1PS50969 FCP1 homology domain profile.CTDS1_HUMAN86-244  1A:86-244

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000002730625aENSE00001038975chr2:219264478-219264880403CTDS1_HUMAN1-23230--
1.9cENST000002730629cENSE00001038976chr2:219266287-219266435149CTDS1_HUMAN23-72500--
1.10aENST0000027306210aENSE00001038973chr2:219266834-219266938105CTDS1_HUMAN73-107351A:76-10732
1.11aENST0000027306211aENSE00001038977chr2:219267072-21926712857CTDS1_HUMAN108-126191A:108-12619
1.12bENST0000027306212bENSE00001621424chr2:219267758-21926785093CTDS1_HUMAN127-157311A:127-15731
1.13cENST0000027306213cENSE00001038974chr2:219267955-219268140186CTDS1_HUMAN158-219621A:158-21962
1.14fENST0000027306214fENSE00000965954chr2:219269020-2192706641645CTDS1_HUMAN220-261421A:220-25637

(-) 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:181
 aligned with CTDS1_HUMAN | Q9GZU7 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:181
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
          CTDS1_HUMAN    76 VQYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLRQ 256
               SCOP domains d1ta0a_ A: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1, NRAMP1                                                                                        SCOP domains
               CATH domains 1ta0A00 A:76-256  [code=3.40.50.1000, no name defined]                                                                                                                                CATH domains
               Pfam domains ---------------NIF-1ta0A01 A:91-251                                                                                                                                             ----- Pfam domains
         Sec.struct. author ........hhhhh...eeee......eeee........eeeeeee..eeeeeeeee..hhhhhhhhhhhhheeeee...hhhhhhhhhhhhh....eeeeehhhhheee..eee.hhhhh..hhh.eeee..hhhhhh.hhhhh............hhhhhhhhhhhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------FCP1  PDB: A:86-244 UniProt: 86-244                                                                                                                            ------------ PROSITE
               Transcript 1 Exon 1.10a  PDB: A:76-107       Exon 1.11a         Exon 1.12b  PDB: A:127-157     Exon 1.13c  PDB: A:158-219 UniProt: 158-219                   Exon 1.14f  PDB: A:220-256            Transcript 1
                 1ta0 A  76 MQYLLPEAKAQDSDKICVVIdLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRESCVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPFFEQLSRVDDVYSVLRQ 256
                                    85        95|      105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
                                               96-BFD                                                                                                                                                            

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CTDS1_HUMAN | Q9GZU7)
molecular function
    GO:0008420    CTD phosphatase activity    Catalysis of the reaction: phospho-(DNA-directed RNA polymerase) + H2O = (DNA-directed RNA polymerase) + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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).
biological process
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0050768    negative regulation of neurogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    BFD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ta0)
 

(-) 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
  1ta0
    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
  CTDS1_HUMAN | Q9GZU7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.16
    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
  CTDS1_HUMAN | Q9GZU7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CTDS1_HUMAN | Q9GZU71t9z 2ghq 2ght 3l0b 3l0c 3l0y 3pgl 4ygy 4yh1

(-) Related Entries Specified in the PDB File

1t9z