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(-) Description

Title :  SOLUTION STRUCTURE OF THE BSD DOMAIN OF HUMAN TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT
 
Authors :  M. Yoneyama, N. Tochio, S. Koshiba, S. Watabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 30 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Btf2-P62, General Transcription Factor Iih Polypeptide 1, Nuclear Protein, Transcription Regulation, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yoneyama, N. Tochio, S. Koshiba, S. Watabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The Bsd Domain Of Human Tfiih Basal Transcription Factor Complex P62 Subunit
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP051212-11
    Expression System Vector TypePLASMID
    FragmentBSD DOMAIN
    GeneGTF2H1, BTF2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymBASIC TRANSCRIPTION FACTOR 62 KDA SUBUNIT, BTF2- P62, GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DII)

(-) Sites  (0, 0)

(no "Site" information available for 2DII)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DII)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BSDPS50858 BSD domain profile.TF2H1_HUMAN99-154
180-232
  1A:8-59
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1gENST000002659631gENSE00002143325chr11:18344143-18344287145TF2H1_HUMAN-00--
1.4bENST000002659634bENSE00002171519chr11:18354607-18354775169TF2H1_HUMAN1-52520--
1.5cENST000002659635cENSE00000886580chr11:18357301-18357493193TF2H1_HUMAN52-116651A:1-21 (gaps)58
1.7aENST000002659637aENSE00000886581chr11:18359656-18359821166TF2H1_HUMAN116-171561A:21-6141
1.8ENST000002659638ENSE00001597724chr11:18361111-1836120494TF2H1_HUMAN172-203320--
1.9ENST000002659639ENSE00001742103chr11:18362808-18362957150TF2H1_HUMAN203-253510--
1.10ENST0000026596310ENSE00001748719chr11:18363075-1836315480TF2H1_HUMAN253-279270--
1.11bENST0000026596311bENSE00001692627chr11:18369135-18369262128TF2H1_HUMAN280-322430--
1.12aENST0000026596312aENSE00001662355chr11:18369379-1836946688TF2H1_HUMAN322-351300--
1.13bENST0000026596313bENSE00001609933chr11:18373428-1837351689TF2H1_HUMAN352-381300--
1.14cENST0000026596314cENSE00001683216chr11:18373876-18373993118TF2H1_HUMAN381-420400--
1.15bENST0000026596315bENSE00001765402chr11:18379499-1837958991TF2H1_HUMAN421-451310--
1.16aENST0000026596316aENSE00001676092chr11:18380072-18380187116TF2H1_HUMAN451-489390--
1.17ENST0000026596317ENSE00001763947chr11:18382162-1838225493TF2H1_HUMAN490-520310--
1.18dENST0000026596318dENSE00001106704chr11:18387330-183885771248TF2H1_HUMAN521-548280--

(-) 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:61
 aligned with TF2H1_HUMAN | P32780 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:98
                                    68        78        88        98       108       118       128       138       148        
          TF2H1_HUMAN    59 GKAKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAEEFWANRLNVNATDSSS 156
               SCOP domains --------------------------------------------d2diia1 A:8-55                                  ------ SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------......-----------------.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------BSD  PDB: A:8-59 UniProt: 99-154                        -- PROSITE
           Transcript 1 (1) Exon 1.5c  PDB: A:1-21 (gaps) UniProt: 52-116 [INCOMPLETE]---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.7a  PDB: A:21-61 UniProt: 116-171  Transcript 1 (2)
                 2dii A   1 G--------------------SSGSSG-----------------FKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAEEFWANRLNVNSGPSSG  61
                            |        -         - |    |  -         -    |   13        23        33        43        53        
                            |                    2    7                 8                                                     
                            1                                                                                                 

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (TF2H1_HUMAN | P32780)
molecular function
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0008353    RNA polymerase II carboxy-terminal domain kinase activity    Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0000717    nucleotide-excision repair, DNA duplex unwinding    The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006295    nucleotide-excision repair, DNA incision, 3'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0006294    nucleotide-excision repair, preincision complex assembly    The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0006293    nucleotide-excision repair, preincision complex stabilization    The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006363    termination of RNA polymerase I transcription    The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
    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: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:0006361    transcription initiation from RNA polymerase I promoter    Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I 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: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:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
cellular component
    GO:0000439    core TFIIH complex    The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
    GO:0005675    holo TFIIH complex    A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
    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
        TF2H1_HUMAN | P327801pfj 2rnr 2ruk 2rvb 5gow

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