BMRB Entry 36405

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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/BMR36405
MolProbity Validation Chart

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Title:
Solution structure of RPB6, common subunit of RNA polymerases I, II, and III
Deposition date:
2021-01-05
Original release date:
2022-01-24
Authors:
Okuda, M.; Nishimura, Y.
Citation:

Citation: Okuda, M.; Suwa, T.; Suzuki, H.; Yamaguchi, Y.; Nishimura, Y.. "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.

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

Data sets:
Data typeCount
13C chemical shifts548
15N chemical shifts136
1H chemical shifts825
heteronuclear NOE values108

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_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

Samples:

sample_1: RPB6, [U-100% 13C; U-100% 15N], 2.0 mM; potassium phosphate 20 mM; NaCl 25 mM; d-DTT, [U-2H], 5 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: RPB6, [U-100% 13C; U-100% 15N], 2.0 mM; potassium phosphate 20 mM; NaCl 25 mM; d-DTT, [U-2H], 5 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 HN(CO)HBsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D HN(CO)CGsample_1isotropicsample_conditions_1
3D HNCGsample_1isotropicsample_conditions_1
3D CC(CO)NHsample_1isotropicsample_conditions_1
3D HCC(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

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

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