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(-) Description

Title :  SOLUTION STRUCTURE OF THE ZINC FINGER DOMAIN OF TFIIE ALPHA
 
Authors :  M. Okuda, A. Tanaka, Y. Arai, M. Satoh, H. Okamura, A. Nagadoi, F. Hanaoka, Y. Ohkuma, Y. Nishimura
Date :  18 Mar 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zinc Finger, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Okuda, A. Tanaka, Y. Arai, M. Satoh, H. Okamura, A. Nagadoi, F. Hanaoka, Y. Ohkuma, Y. Nishimura
A Novel Zinc Finger Structure In The Large Subunit Of Human General Transcription Factor Tfiie.
J. Biol. Chem. V. 279 51395 2004
PubMed-ID: 15385556  |  Reference-DOI: 10.1074/JBC.M404722200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION INITIATION FACTOR IIE, ALPHA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11D
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER DOMAIN
    Gene: GTF2E1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TFIIE-ALPHA, GENERAL TRANSCRIPTION FACTOR IIE 56 KDA SUBUNIT, GENERAL TRANSCRIPTION FACTOR TFIIE ALPHA

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:129 , CYS A:132 , CYS A:154 , CYS A:157 , THR A:159BINDING SITE FOR RESIDUE ZN A 175

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VD4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VD4)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002838751bENSE00001559931chr3:120461579-12046164163T2EA_HUMAN-00--
1.3cENST000002838753cENSE00001012283chr3:120469370-120469847478T2EA_HUMAN1-1501501A:113-15038
1.4ENST000002838754ENSE00001012285chr3:120489575-120489776202T2EA_HUMAN150-217681A:150-17425
1.5bENST000002838755bENSE00001074548chr3:120495270-120495511242T2EA_HUMAN217-298820--
1.6ENST000002838756ENSE00001206456chr3:120499890-1205019162027T2EA_HUMAN298-4391420--

(-) 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:62
 aligned with T2EA_HUMAN | P29083 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:62
                                   122       132       142       152       162       172  
           T2EA_HUMAN   113 RIETDERDSTNRASFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEEDESAMPKKDAR 174
               SCOP domains d1vd4a_ A: Transcription initiation factor TFIIE-alpha         SCOP domains
               CATH domains 1vd4A00 A:113-174 Zinc/RING finger domain, C3HC4 (zinc finger) CATH domains
               Pfam domains TFIIE_alpha---TF_Zn_Ribbon-1vd4A02 A:127-174                   Pfam domains
         Sec.struct. author .............eeee....eee.hhhhhhhee....eeee....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3c  PDB: A:113-150 [INCOMPLETE]------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.4  PDB: A:150-174  Transcript 1 (2)
                 1vd4 A 113 RIETDERDSTNRASFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEEDESAMPKKDAR 174
                                   122       132       142       152       162       172
   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: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: HTH (544)
(-)
Clan: Zn_Beta_Ribbon (109)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (T2EA_HUMAN | P29083)
molecular function
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042795    snRNA transcription from RNA polymerase II promoter    The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
    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: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).
    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.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        T2EA_HUMAN | P29083: 2jtx 2rnq 2rnr 5gpy 5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd

(-) Related Entries Specified in the PDB File

1d8j SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BATA (20 STRUCTURES)
1d8k SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BATA (AVERAGE STRUCTURE)