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Entry version 125 (17 Jun 2020)
Sequence version 1 (01 Nov 1998)
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Protein

General transcription and DNA repair factor IIH subunit tfb4

Gene

tfb4

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to TFIIK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module TFIIK controls the initiation of transcription.By similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri265 – 282C4-typeAdd BLAST18

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processDNA damage, DNA repair, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SPO-113418 Formation of the Early Elongation Complex
R-SPO-5696395 Formation of Incision Complex in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-674695 RNA Polymerase II Pre-transcription Events
R-SPO-6781823 Formation of TC-NER Pre-Incision Complex
R-SPO-6782135 Dual incision in TC-NER
R-SPO-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SPO-72086 mRNA Capping
R-SPO-73772 RNA Polymerase I Promoter Escape
R-SPO-73776 RNA Polymerase II Promoter Escape
R-SPO-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SPO-75953 RNA Polymerase II Transcription Initiation
R-SPO-75955 RNA Polymerase II Transcription Elongation
R-SPO-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SPO-77075 RNA Pol II CTD phosphorylation and interaction with CE

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
General transcription and DNA repair factor IIH subunit tfb4
Short name:
TFIIH subunit tfb4
Alternative name(s):
RNA polymerase II transcription factor B subunit 4
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:tfb4
ORF Names:pi078, SPBC30B4.07c
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri284812 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002485 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome II

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:SPBC30B4.07c

Schizosaccharomyces pombe database

More...
PomBasei
SPBC30B4.07c tfb4

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001192731 – 297General transcription and DNA repair factor IIH subunit tfb4Add BLAST297

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
O74366

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
O74366

PRoteomics IDEntifications database

More...
PRIDEi
O74366

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the 7-subunit TFIIH core complex composed of XPB/ptr8, XPD/rad15, ssl1, tfb1, tfb2, tfb4 and tfb5, which is active in NER. The core complex associates with the 3-subunit CTD-kinase module TFIIK composed of mcs2/cyclin H, mcs6/cdk7 and pmh1/tfb3 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
276872, 2 interactors

Protein interaction database and analysis system

More...
IntActi
O74366, 1 interactor

STRING: functional protein association networks

More...
STRINGi
4896.SPBC30B4.07c.1

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the TFB4 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri265 – 282C4-typeAdd BLAST18

Keywords - Domaini

Zinc-finger

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_040211_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O74366

KEGG Orthology (KO)

More...
KOi
K03143

Identification of Orthologs from Complete Genome Data

More...
OMAi
MNIFFAA

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O74366

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.410, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR004600 TFIIH_Tfb4/GTF2H3
IPR036465 vWFA_dom_sf

The PANTHER Classification System

More...
PANTHERi
PTHR12831 PTHR12831, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03850 Tfb4, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00627 tfb4, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

O74366-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDEFQTLKQN ASWDISEDAN DTPSLLVVIL DANPASWYSL SKKVPVSKVL
60 70 80 90 100
ADITVFLNAH LAFHHDNRVA VLASHSDKVE YLYPSIAPEQ KVAEVDPTKE
110 120 130 140 150
ANTYRKFREV DDLVLSGMKR LMSSTDKVSR KTMISGALSR ALAYINQVQN
160 170 180 190 200
KNTLRSRILI FSLTGDVALQ YIPTMNCIFC AQKKNIPINV CNIEGGTLFL
210 220 230 240 250
EQAADATGGI YLKVDNPKGL LQYLMMSLFP DQNLRKHLNT PNQANVDFRA
260 270 280 290
TCFCHKKVLD IGFVCSVCLS IFCEPRVHCS TCHTKFTVEP MSKKLHT
Length:297
Mass (Da):33,277
Last modified:November 1, 1998 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i70A88655E58D2D02
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti288 – 297VEPMSKKLHT → DQTISLRGIHK in BAA21460 (PubMed:10620777).Curated10

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AB004539 Genomic DNA Translation: BAA21460.1
CU329671 Genomic DNA Translation: CAA20320.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T40173

NCBI Reference Sequences

More...
RefSeqi
NP_595532.1, NM_001021442.2

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
SPBC30B4.07c.1; SPBC30B4.07c.1:pep; SPBC30B4.07c

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
2540343

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
spo:SPBC30B4.07c

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB004539 Genomic DNA Translation: BAA21460.1
CU329671 Genomic DNA Translation: CAA20320.1
PIRiT40173
RefSeqiNP_595532.1, NM_001021442.2

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

BioGRIDi276872, 2 interactors
IntActiO74366, 1 interactor
STRINGi4896.SPBC30B4.07c.1

Proteomic databases

MaxQBiO74366
PaxDbiO74366
PRIDEiO74366

Genome annotation databases

EnsemblFungiiSPBC30B4.07c.1; SPBC30B4.07c.1:pep; SPBC30B4.07c
GeneIDi2540343
KEGGispo:SPBC30B4.07c

Organism-specific databases

EuPathDBiFungiDB:SPBC30B4.07c
PomBaseiSPBC30B4.07c tfb4

Phylogenomic databases

HOGENOMiCLU_040211_0_0_1
InParanoidiO74366
KOiK03143
OMAiMNIFFAA
PhylomeDBiO74366

Enzyme and pathway databases

ReactomeiR-SPO-113418 Formation of the Early Elongation Complex
R-SPO-5696395 Formation of Incision Complex in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-674695 RNA Polymerase II Pre-transcription Events
R-SPO-6781823 Formation of TC-NER Pre-Incision Complex
R-SPO-6782135 Dual incision in TC-NER
R-SPO-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SPO-72086 mRNA Capping
R-SPO-73772 RNA Polymerase I Promoter Escape
R-SPO-73776 RNA Polymerase II Promoter Escape
R-SPO-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SPO-75953 RNA Polymerase II Transcription Initiation
R-SPO-75955 RNA Polymerase II Transcription Elongation
R-SPO-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SPO-77075 RNA Pol II CTD phosphorylation and interaction with CE

Miscellaneous databases

Protein Ontology

More...
PROi
PR:O74366

Family and domain databases

Gene3Di3.40.50.410, 1 hit
InterProiView protein in InterPro
IPR004600 TFIIH_Tfb4/GTF2H3
IPR036465 vWFA_dom_sf
PANTHERiPTHR12831 PTHR12831, 1 hit
PfamiView protein in Pfam
PF03850 Tfb4, 1 hit
TIGRFAMsiTIGR00627 tfb4, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiTFB4_SCHPO
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O74366
Secondary accession number(s): O13669
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2005
Last sequence update: November 1, 1998
Last modified: June 17, 2020
This is version 125 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
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