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- PDB-5urn: NMR structure of the complex between the PH domain of the Tfb1 su... -

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Basic information

Entry
Database: PDB / ID: 5urn
TitleNMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65
Components
  • RNA polymerase II transcription factor B subunit 1
  • Transcription factor p65
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR TFIIH / TRANSACTIVATION DOMAIN / NUCLEAR FACTOR KAPPA-B / TRANSCRIPTIONAL ACTIVATION / P62/TFB1 SUBUNIT
Function / homology
Function and homology information


prolactin signaling pathway / phosphatidylinositol-5-phosphate binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / nucleotide-excision repair factor 3 complex / response to cobalamin / cellular response to peptidoglycan ...prolactin signaling pathway / phosphatidylinositol-5-phosphate binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / nucleotide-excision repair factor 3 complex / response to cobalamin / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / phosphatidylinositol-3-phosphate binding / Interleukin-1 processing / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cellular response to interleukin-6 / actinin binding / non-canonical NF-kappaB signal transduction / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / positive regulation of amyloid-beta formation / TP53 Regulates Transcription of DNA Repair Genes / 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 / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / phosphate ion binding / positive regulation of T cell receptor signaling pathway / RNA Polymerase I Promoter Escape / cellular response to lipoteichoic acid / response to muramyl dipeptide / Gap-filling DNA repair synthesis and ligation in TC-NER / TRAF6 mediated NF-kB activation / positive regulation of vascular endothelial growth factor production / Transcriptional Regulation by VENTX / cellular response to angiotensin / The NLRP3 inflammasome / Dual incision in TC-NER / general transcription initiation factor binding / cellular response to interleukin-1 / canonical NF-kappaB signal transduction / response to cAMP / hair follicle development / NF-kappaB binding / neuropeptide signaling pathway / response to amino acid / cellular defense response / Purinergic signaling in leishmaniasis infection / RNA polymerase II core promoter sequence-specific DNA binding / transcription by RNA polymerase I / response to muscle stretch / response to cytokine / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / CD209 (DC-SIGN) signaling / negative regulation of insulin receptor signaling pathway / NF-kB is activated and signals survival / response to interleukin-1 / response to progesterone / negative regulation of miRNA transcription / negative regulation of angiogenesis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / animal organ morphogenesis / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / protein catabolic process / liver development / positive regulation of non-canonical NF-kappaB signal transduction
Similarity search - Function
Transcription factor RelA (p65) / 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 / NF-kappa-B/Dorsal ...Transcription factor RelA (p65) / 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 / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / p53-like transcription factor, DNA-binding / PH-like domain superfamily / Immunoglobulin E-set / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB1 / Transcription factor p65
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLecoq, L. / Omichinski, J.G. / Raiola, L. / Cyr, N. / Chabot, P. / Arseneault, G. / Legault, P.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-kappa B and transcription regulatory factors.
Authors: Lecoq, L. / Raiola, L. / Chabot, P.R. / Cyr, N. / Arseneault, G. / Legault, P. / Omichinski, J.G.
History
DepositionFeb 11, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 8, 2017ID: 2N22
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Derived calculations
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA polymerase II transcription factor B subunit 1
B: Transcription factor p65


Theoretical massNumber of molelcules
Total (without water)16,2822
Polymers16,2822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area10330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 260structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein RNA polymerase II transcription factor B subunit 1 / General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase ...General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit


Mass: 12903.701 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, UNP RESIDUES 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TFB1, YDR311W, D9740.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P32776
#2: Protein/peptide Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 3378.591 Da / Num. of mol.: 1 / Fragment: TRANSACTIVATION DOMAIN 1, UNP RESIDUES 521-551 / Mutation: L523Y
Source method: isolated from a genetically manipulated source
Details: The first GS residues come from a purification TAG.
Source: (gene. exp.) Homo sapiens (human) / Gene: RELA, NFKB3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04206

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic32D 1H-13C HSQC aliphatic
133isotropic32D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
193isotropic33D 1H-13C NOESY
1103isotropic33D INTERMOLECULAR NOESY
1111isotropic13D C(CO)NH
1122isotropic12D 1H-15N HSQC
1132isotropic12D 1H-13C HSQC aliphatic
1142isotropic12D 1H-13C HSQC aromatic
1152isotropic13D HNCO
1162isotropic13D HN(CA)CB
1172isotropic13D 1H-15N NOESY
1184isotropic33D 1H-13C NOESY
1194isotropic33D INTERMOLECULAR NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 90% H2O/10% D2O13C-15N labeled Tfb1 with 2 equivalents of unlabeled p65-TA1.Tfb1-p6590% H2O/10% D2O
solution30.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 100% D2O13C-15N labeled Tfb1 with 2 equivalents of unlabeled p65-TA1 in D20.Tfb1-p65-D2O100% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 90% H2O/10% D2O13C-15N labeled p65-TA1 with 2 equivalents of unlabeled Tfb1.p65-Tfb190% H2O/10% D2O
solution40.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 100% D2O13C-15N labeled p65-TA1 with 2 equivalents of unlabeled Tfb1 in D2O.p65-Tfb1-D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMRNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1[U-99% 13C; U-99% 15N]1
1.6 mMTRANSCRIPTION FACTOR P65natural abundance1
0.8 mMRNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1[U-99% 13C; U-99% 15N]3
1.6 mMTRANSCRIPTION FACTOR P65natural abundance3
0.8 mMTRANSCRIPTION FACTOR P65[U-99% 13C; U-99% 15N]2
1.6 mMRNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1natural abundance2
0.8 mMTRANSCRIPTION FACTOR P65[U-99% 13C; U-99% 15N]4
1.6 mMRNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1natural abundance4
Sample conditionsIonic strength: 0 mM / Label: Condition1 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER A. T. ET.AL.refinement
YASARAKRIEGER ET ALrefinement
ARIAstructure solution
CCPNMRstructure solution
VNMRstructure solution
NMRPipestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SIDECHAINS OPTIMIZATION WITH YASARA
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 260 / Conformers submitted total number: 20

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