Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  CONSERVED DOMAIN COMMON TO TRANSCRIPTION FACTORS TFIIS, ELONGIN A, CRSP70
 
Authors :  V. Booth, C. Koth, A. M. Edwards, C. H. Arrowsmith, Northeast Structural Genomics Consortium (Nesg)
Date :  21 Mar 00  (Deposition) - 03 May 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Helix-Bundle, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Booth, C. Koth, A. M. Edwards, C. H. Arrowsmith
Structure Of A Conserved Domain Common To The Transcription Factors Tfiis, Elongin A, And Crsp70
J. Biol. Chem. V. 275 31266 2000
PubMed-ID: 10811649  |  Reference-DOI: 10.1074/JBC.M002595200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION ELONGATION FACTOR S-II
    Chains: A
    Engineered: YES
    Expression System: BACTERIA
    Expression System Common: EUBACTERIA
    Expression System Taxid: 2
    Fragment: DOMAIN I
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1EO0)

(-) Sites  (0, 0)

(no "Site" information available for 1EO0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EO0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EO0)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TFIIS_NPS51319 TFIIS N-terminal domain profile.TFS2_YEAST5-79  1A:5-77

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL043W1YGL043W.1VII:417487-418416930TFS2_YEAST1-3093091A:1-7777

(-) 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:77
 aligned with TFS2_YEAST | P07273 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:77
                                    10        20        30        40        50        60        70       
            TFS2_YEAST    1 MDSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAIN 77
               SCOP domains d1eo0a_ A: Transcription elongation factor TFIIS N-domain                     SCOP domains
               CATH domains 1eo0A00 A:1-77  [code=1.20.930.10, no name defined]                           CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----TFIIS_N  PDB: A:5-77 UniProt: 5-79                                        PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-77 UniProt: 1-309 [INCOMPLETE]                             Transcript 1
                  1eo0 A  1 MDSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAIN 77
                                    10        20        30        40        50        60        70
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EO0)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (TFS2_YEAST | P07273)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
    GO:0001012    RNA polymerase II regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. 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.
    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: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:0001139    transcription factor activity, core RNA polymerase II recruiting    Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051123    RNA polymerase II transcriptional preinitiation complex assembly    The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
    GO:0001193    maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter    Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter.
    GO:0045899    positive regulation of RNA polymerase II transcriptional preinitiation complex assembly    Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0032784    regulation of DNA-templated transcription, elongation    Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
    GO:0031440    regulation of mRNA 3'-end processing    Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule.
    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.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042797    tRNA transcription from RNA polymerase III promoter    The synthesis of transfer RNA (tRNA) from a DNA template by RNA Polymerase III (Pol III), originating at a Pol III promoter.
    GO:0031564    transcription antitermination    Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
    GO:0006362    transcription elongation from RNA polymerase I promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006383    transcription from RNA polymerase III promoter    The synthesis of RNA from a DNA template by RNA polymerase III, originating at an RNAP III promoter.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 1eo0)
 
  Sites
(no "Sites" information available for 1eo0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1eo0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1eo0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TFS2_YEAST | P07273
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TFS2_YEAST | P07273
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TFS2_YEAST | P07273: 1enw 1pqv 1y1v 1y1y 3gtm 3po3 5fmf

(-) Related Entries Specified in the PDB File

1enw RELATED ID: YT101 RELATED DB: TARGETDB