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- PDB-2rvb: Solution structure of the complex between XPC acidic domain and T... -

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Basic information

Entry
Database: PDB / ID: 2rvb
TitleSolution structure of the complex between XPC acidic domain and TFIIH p62 PH domain
Components
  • DNA repair protein complementing XP-C cells
  • General transcription factor IIH subunit 1
KeywordsDNA BINDING PROTEIN/TRANSCRIPTION / DNA REPAIR / HUMAN XPC / ACIDIC DOMAIN / GENERAL TRANSCRIPTION FACTOR / HUMAN TFIIH P62 / PH DOMAIN / DNA BINDING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / DNA damage sensor activity / response to auditory stimulus / bubble DNA binding / UV-damage excision repair / transcription factor TFIIH holo complex ...heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / DNA damage sensor activity / response to auditory stimulus / bubble DNA binding / UV-damage excision repair / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / site of DNA damage / RNA Polymerase I Transcription Initiation / mismatch repair / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / hormone-mediated signaling pathway / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / DNA Damage Recognition in GG-NER / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / transcription coactivator activity / response to xenobiotic stimulus / DNA repair / intracellular membrane-bounded organelle / chromatin binding / chromatin / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rad4 beta-hairpin domain 2 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 ...Rad4 beta-hairpin domain 2 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Transglutaminase-like superfamily / 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 / Papain-like cysteine peptidase superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 1 / DNA repair protein complementing XP-C cells
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: Structure / Year: 2015
Title: Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC.
Authors: Okuda, M. / Kinoshita, M. / Kakumu, E. / Sugasawa, K. / Nishimura, Y.
History
DepositionJul 1, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein complementing XP-C cells
B: General transcription factor IIH subunit 1


Theoretical massNumber of molelcules
Total (without water)18,3762
Polymers18,3762
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA repair protein complementing XP-C cells / / Xeroderma pigmentosum group C-complementing protein / p125


Mass: 5925.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPC, XPCC / Production host: Escherichia coli (E. coli) / References: UniProt: Q01831
#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
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HBHA(CO)NH
1623D (H)CCH-TOCSY
1722D 1H-13C HSQC aromatic
1813D HNHB
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11132D 1H-15N HSQC
11242D 1H-13C HSQC
11333D CBCA(CO)NH
11433D HNCO
11533D HBHA(CO)NH
11643D (H)CCH-TOCSY
11742D 1H-13C HSQC aromatic
11833D HNHB
11933D 1H-15N NOESY
12043D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-99% 13C; U-99% 15N] XPC acidic domain-1, 0.48 mM TFIIH p62 PH domain-2, 20 mM potassium phosphate-3, 5 mM [U-2H] DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-99% 13C; U-99% 15N] XPC acidic domain-5, 0.48 mM TFIIH p62 PH domain-6, 20 mM potassium phosphate-7, 5 mM [U-2H] DTT-8, 100% D2O100% D2O
30.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-9, 0.48 mM XPC acidic domain-10, 20 mM potassium phosphate-11, 5 mM [U-2H] DTT-12, 90% H2O/10% D2O90% H2O/10% D2O
40.4 mM [U-99% 13C; U-99% 15N] TFIIH p62 PH domain-13, 0.48 mM XPC acidic domain-14, 20 mM potassium phosphate-15, 5 mM [U-2H] DTT-16, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMXPC acidic domain-1[U-99% 13C; U-99% 15N]1
0.48 mMTFIIH p62 PH domain-21
20 mMpotassium phosphate-31
5 mMDTT-4[U-2H]1
0.4 mMXPC acidic domain-5[U-99% 13C; U-99% 15N]2
0.48 mMTFIIH p62 PH domain-62
20 mMpotassium phosphate-72
5 mMDTT-8[U-2H]2
0.4 mMTFIIH p62 PH domain-9[U-99% 13C; U-99% 15N]3
0.48 mMXPC acidic domain-103
20 mMpotassium phosphate-113
5 mMDTT-12[U-2H]3
0.4 mMTFIIH p62 PH domain-13[U-99% 13C; U-99% 15N]4
0.48 mMXPC acidic domain-144
20 mMpotassium phosphate-154
5 mMDTT-16[U-2H]4
Sample conditionsIonic strength: 0.02 / pH: 6.8 / Pressure: ambient atm / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance7002
Bruker AvanceBrukerAvance6003

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MolmolKoradi, Billeter and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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