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(-) Description

Title :  SOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN
 
Authors :  H. -T. Chen, P. Legault, J. Glushka, J. G. Omichinski, R. A. Scott
Date :  08 Dec 99  (Deposition) - 18 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Zinc Ribbon, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. T. Chen, P. Legault, J. Glushka, J. G. Omichinski, R. A. Scott
Structure Of A (Cys3His) Zinc Ribbon, A Ubiquitous Motif In Archaeal And Eucaryal Transcription.
Protein Sci. V. 9 1743 2000
PubMed-ID: 11045620
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR II B (TFIIB)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (25x)

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:15 , HIS A:18 , CYS A:34 , CYS A:37BINDING SITE FOR RESIDUE ZN A 60

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DL6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DL6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011977P19STF2B_HUMANPolymorphism1804499AP19S

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_TFIIBPS51134 Zinc finger TFIIB-type profile.TF2B_HUMAN11-42  1A:11-42

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003705001cENSE00001452875chr1:89357301-89357166136TF2B_HUMAN1-661A:2-65
1.3bENST000003705003bENSE00001158820chr1:89353050-89352944107TF2B_HUMAN6-42371A:6-4237
1.4cENST000003705004cENSE00000932079chr1:89329797-89329664134TF2B_HUMAN42-86451A:42-5918
1.5aENST000003705005aENSE00000932078chr1:89325969-89325823147TF2B_HUMAN87-135490--
1.6ENST000003705006ENSE00000932077chr1:89325694-89325565130TF2B_HUMAN136-179440--
1.8dENST000003705008dENSE00000932076chr1:89323170-89322889282TF2B_HUMAN179-273950--
1.9bENST000003705009bENSE00001158811chr1:89319029-89318615415TF2B_HUMAN273-316440--

(-) 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:58
 aligned with TF2B_HUMAN | Q00403 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:58
                                    11        21        31        41        51        
            TF2B_HUMAN    2 ASTSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDK 59
               SCOP domains d1dl6a_ A:                                                 SCOP domains
               CATH domains 1dl6A00 A:2-59  [code=2.20.25.10, no name defined]         CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee......ee......ee.................. Sec.struct. author
                 SAPs(SNPs) -----------------S---------------------------------------- SAPs(SNPs)
                    PROSITE ---------ZF_TFIIB  PDB: A:11-42          ----------------- PROSITE
           Transcript 1 (1) 1.1c -----------------------------------Exon 1.4c          Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.3b  PDB: A:6-42 UniProt: 6-42 ----------------- Transcript 1 (2)
                  1dl6 A  2 ASTSRLDALPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDK 59
                                    11        21        31        41        51        

   Legend:   → Mismatch (orange background)
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    → 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  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DL6)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (TF2B_HUMAN | Q00403)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0017025    TBP-class protein binding    Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. 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: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:0046966    thyroid hormone receptor binding    Interacting selectively and non-covalently with a thyroid hormone receptor.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core 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. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        TF2B_HUMAN | Q004031c9b 1rly 1ro4 1tfb 1vol 2phg 5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd

(-) Related Entries Specified in the PDB File

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