BMRB Entry 36406

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36406
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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Title:
Solution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain
Deposition date:
2021-01-05
Original release date:
2025-10-25
Authors:
Okuda, M.; Nishimura, Y.
Citation:

Citation: Okuda, Masahiko; Suwa, Tetsufumi; Suzuki, Hidefumi; Yamaguchi, Yuki; Nishimura, Yoshifumi. "Three human RNA polymerases interact with TFIIH via a common RPB6 subunit."  Nucleic Acids Res. 50, 1-16 (2022).
PubMed: 34268577

Assembly members:

Assembly members:
DNA-directed RNA polymerases I, II, and III subunit RPABC2, polymer, 130 residues, 14773.305 Da.
cDNA, FLJ93435, highly similar to Homo sapiens general transcription factor IIH, polypeptide 1 (62kD subunit) (GTF2H1), mRNA, polymer, 111 residues, 12588.593 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA-directed RNA polymerases I, II, and III subunit RPABC2: GSHMSDNEDNFDGDDFDDVE EDEGLDDLENAEEEGQENVE ILPSGERPQANQKRITTPYM TKYERARVLGTRALQIAMCA PVMVELEGETDPLLIAMKEL KARKIPIIIRRYLPDGSYED WGVDELIITD
cDNA, FLJ93435, highly similar to Homo sapiens general transcription factor IIH, polypeptide 1 (62kD subunit) (GTF2H1), mRNA: GSHMATSSEEVLLIVKKVRQ KKQDGALYLMAERIAWAPEG KDRFTISHMYADIKCQKISP EGKAKIQLQLVLHAGDTTNF HFSNESTAVKERDAVKDLLQ QLLPKFKRKAN

Data sets:
Data typeCount
13C chemical shifts1008
15N chemical shifts245
1H chemical shifts1509

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 130 residues - 14773.305 Da.

1   GLYSERHISMETSERASPASNGLUASPASN
2   PHEASPGLYASPASPPHEASPASPVALGLU
3   GLUASPGLUGLYLEUASPASPLEUGLUASN
4   ALAGLUGLUGLUGLYGLNGLUASNVALGLU
5   ILELEUPROSERGLYGLUARGPROGLNALA
6   ASNGLNLYSARGILETHRTHRPROTYRMET
7   THRLYSTYRGLUARGALAARGVALLEUGLY
8   THRARGALALEUGLNILEALAMETCYSALA
9   PROVALMETVALGLULEUGLUGLYGLUTHR
10   ASPPROLEULEUILEALAMETLYSGLULEU
11   LYSALAARGLYSILEPROILEILEILEARG
12   ARGTYRLEUPROASPGLYSERTYRGLUASP
13   TRPGLYVALASPGLULEUILEILETHRASP

Entity 2, entity_2 111 residues - 12588.593 Da.

1   GLYSERHISMETALATHRSERSERGLUGLU
2   VALLEULEUILEVALLYSLYSVALARGGLN
3   LYSLYSGLNASPGLYALALEUTYRLEUMET
4   ALAGLUARGILEALATRPALAPROGLUGLY
5   LYSASPARGPHETHRILESERHISMETTYR
6   ALAASPILELYSCYSGLNLYSILESERPRO
7   GLUGLYLYSALALYSILEGLNLEUGLNLEU
8   VALLEUHISALAGLYASPTHRTHRASNPHE
9   HISPHESERASNGLUSERTHRALAVALLYS
10   GLUARGASPALAVALLYSASPLEULEUGLN
11   GLNLEULEUPROLYSPHELYSARGLYSALA
12   ASN

Samples:

sample_1: RPB6, [U-100% 13C; U-100% 15N], 0.38 mM; TFIIH p62 0.76 mM; d-DTT, [U-2H], 5 mM; NaCl 25 mM; potassium phosphate 20 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: RPB6, [U-100% 13C; U-100% 15N], 0.38 mM; TFIIH p62 0.76 mM; d-DTT, [U-2H], 5 mM; NaCl 25 mM; potassium phosphate 20 mM; D2O, [U-2H], 100%

sample_3: RPB6 0.76 mM; TFIIH p62, [U-100% 13C; U-100% 15N], 0.38 mM; d-DTT, [U-2H], 5 mM; NaCl 25 mM; potassium phosphate 20 mM; H2O 90%; D2O, [U-2H], 10%

sample_4: RPB6 0.76 mM; TFIIH p62, [U-100% 13C; U-100% 15N], 0.38 mM; d-DTT, [U-2H], 5 mM; NaCl 25 mM; potassium phosphate 20 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 25 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromasample_4isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D CBCANHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D HNCAsample_3isotropicsample_conditions_1
3D HN(CO)CAsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HBHANHsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1

Software:

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - peak picking

NMRView, Johnson, One Moon Scientific - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker AVANCE III HD 600 MHz
  • Bruker AVANCE III HD 950 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks