[English] 日本語
Yorodumi
- PDB-5gow: Solution structure of the complex between DP1 acidic region and T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gow
TitleSolution structure of the complex between DP1 acidic region and TFIIH p62 PH domain
Components
  • DP1
  • General transcription factor IIH subunit 1
KeywordsTRANSCRIPTION / Transcription factor / General transcription factor / Cell cycle / Transcription activation / Solution structure
Function / homology
Function and homology information


negative regulation of fat cell proliferation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / Activation of PUMA and translocation to mitochondria / nuclear thyroid hormone receptor binding ...negative regulation of fat cell proliferation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / Activation of PUMA and translocation to mitochondria / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / G1/S-Specific Transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / G0 and Early G1 / Tat-mediated elongation of the HIV-1 transcript / Cyclin E associated events during G1/S transition / Formation of HIV-1 elongation complex containing HIV-1 Tat / Cyclin A:Cdk2-associated events at S phase entry / Formation of HIV elongation complex in the absence of HIV Tat / hormone-mediated signaling pathway / cis-regulatory region sequence-specific DNA binding / positive regulation of G1/S transition of mitotic cell cycle / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / RNA polymerase II transcription regulator complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / nucleotide-excision repair / Oncogene Induced Senescence / NoRC negatively regulates rRNA expression / transcription by RNA polymerase II / Pre-NOTCH Transcription and Translation / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Transcriptional regulation of granulopoiesis / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Cyclin D associated events in G1 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / heterochromatin formation / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / DNA repair / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / TFIIH p62 subunit, N-terminal ...Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 1 / Transcription factor Dp-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: J. Mol. Biol. / Year: 2016
Title: The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH
Authors: Okuda, M. / Araki, K. / Ohtani, K. / Nishimura, Y.
History
DepositionJul 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DP1
B: General transcription factor IIH subunit 1


Theoretical massNumber of molelcules
Total (without water)14,7292
Polymers14,7292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1980 Å2
ΔGint5 kcal/mol
Surface area6460 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide DP1


Mass: 2279.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14186*PLUS
#2: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 12450.445 Da / Num. of mol.: 1 / Fragment: UNP residues 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P32780

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
141isotropic23D CBCA(CO)NH
151isotropic23D HNCO
161isotropic23D HBHA(CO)NH
171isotropic23D C(CO)NH
181isotropic23D H(CCO)NH
191isotropic13D 1H-15N NOESY
1102isotropic13D 1H-13C NOESY
1113isotropic12D 1H-15N HSQC
1124isotropic12D 1H-13C HSQC
1134isotropic12D 1H-13C HSQC aromatic
1143isotropic23D CBCA(CO)NH
1153isotropic23D HNCO
1163isotropic23D HBHA(CO)NH
1173isotropic23D C(CO)NH
1183isotropic23D H(CCO)NH
1193isotropic13D 1H-15N NOESY
1204isotropic13D 1H-13C NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2ODP1-p6290% H2O/10% D2O
solution20.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2ODP1-p62100% D2O
solution30.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2Op62-DP190% H2O/10% D2O
solution40.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2Op62-DP1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.35 mMDP1[U-99% 13C; U-99% 15N]1
0.42 mMTFIIH p62natural abundance1
0.35 mMDP1[U-99% 13C; U-99% 15N]2
0.42 mMTFIIH p62natural abundance2
0.35 mMTFIIH p62[U-99% 13C; U-99% 15N]3
0.42 mMDP1natural abundance3
0.35 mMTFIIH p62[U-99% 13C; U-99% 15N]4
0.42 mMDP1natural abundance4
Sample conditionsIonic strength: 0.02 M / Label: condition_1 / pH: 6.8 / Pressure: 760 Torr / Temperature: 305 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III6002

-
Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4
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