[English] 日本語
Yorodumi
- PDB-8i53: Solution structure of the PH domain from the Tfb1 subunit of fiss... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i53
TitleSolution structure of the PH domain from the Tfb1 subunit of fission yeast TFIIH
ComponentsGeneral transcription and DNA repair factor IIH subunit tfb1
KeywordsTRANSCRIPTION / Transcription factor Nucleotide excision repair factor Nuclear protein
Function / homology
Function and homology information


Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events ...Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nucleotide-excision repair factor 3 complex / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA polymerase II general transcription initiation factor activity / transcription by RNA polymerase I / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / DNA repair / cytosol / cytoplasm
Similarity search - Function
TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / PH-like domain superfamily
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit tfb1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biosci.Rep. / Year: 2023
Title: Structural polymorphism of the PH domain in TFIIH.
Authors: Okuda, M. / Nishimura, Y.
History
DepositionJan 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: General transcription and DNA repair factor IIH subunit tfb1


Theoretical massNumber of molelcules
Total (without water)12,3051
Polymers12,3051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein General transcription and DNA repair factor IIH subunit tfb1 / TFIIH subunit tfb1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II ...TFIIH subunit tfb1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit / RNA polymerase II transcription factor B subunit 1


Mass: 12304.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: tfb1, SPAC16E8.11c / Production host: Escherichia coli (E. coli) / References: UniProt: O13745

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC
133isotropic12D 1H-13C HSQC aromatic
142isotropic23D CBCA(CO)NH
152isotropic23D HN(CA)CB
162isotropic23D HN(CO)CA
172isotropic23D HNCA
182isotropic23D HNCO
192isotropic23D HN(CA)CO
1102isotropic23D HBHA(CO)NH
1112isotropic23D HBHANH
1122isotropic23D C(CO)NH
1132isotropic23D H(CCO)NH
1142isotropic23D HN(CO)HB
1152isotropic23D HNHB
1162isotropic23D HN(CO)CG
1172isotropic23D HNCG
1181isotropic13D 1H-15N NOESY
1193isotropic13D 1H-13C NOESY
1203isotropic13D 1H-13C NOESY aromatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.9 mM [U-15N] Tfb1, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.9 mM [U-13C; U-15N] Tfb1, 90% H2O/10% D2O13C15N_H20_sample90% H2O/10% D2O
solution30.9 mM [U-13C; U-15N] Tfb1, 100% D2O13C15N_D20_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMTfb1[U-15N]1
0.9 mMTfb1[U-13C; U-15N]2
0.9 mMTfb1[U-13C; U-15N]3
Sample conditionsDetails: 20mM KPB(pH6.8), 5mM d-DTT / Ionic strength: 0 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 bar / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9501
Bruker AVANCE III HDBrukerAVANCE III HD6002

-
Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MAGROKobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, Yokoyamapeak picking
MAGROKobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, Yokoyamachemical shift assignment
NMRViewJJohnson, Blevinspeak picking
NMRViewJJohnson, Blevinschemical shift assignment
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more