BMRB Entry 36546

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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/BMR36546
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Solution structure of the PH domain from the Tfb1 subunit of fission yeast TFIIH
Deposition date:
2023-01-23
Original release date:
2025-11-04
Authors:
Okuda, M.; Nishimura, Y.
Citation:

Citation: Okuda, Masahiko; Nishimura, Yoshifumi. "Structural polymorphism of the PH domain in TFIIH."  Biosci. Rep. 43, .-. (2023).
PubMed: 37340985

Assembly members:

Assembly members:
General transcription and DNA repair factor IIH subunit tfb1, polymer, 111 residues, 12304.934 Da.

Natural source:

Natural source:   Common Name: fission yeast   Taxonomy ID: 4896   Superkingdom: not available   Kingdom: Fungi   Genus/species: Schizosaccharomyces pombe

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
General transcription and DNA repair factor IIH subunit tfb1: GSHMGDRVEALAIFRKKQGV LSIDSRLKWTGEGKTTPSVD IAFDAISNLQTTPASNPKVM IRVFIVVKEGEDPTSLVFHF TGTPNARENCDMITNELRNA IQRQREGSQSK

Data sets:
Data typeCount
13C chemical shifts469
15N chemical shifts120
1H chemical shifts734

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 111 residues - 12304.934 Da.

1   GLYSERHISMETGLYASPARGVALGLUALA
2   LEUALAILEPHEARGLYSLYSGLNGLYVAL
3   LEUSERILEASPSERARGLEULYSTRPTHR
4   GLYGLUGLYLYSTHRTHRPROSERVALASP
5   ILEALAPHEASPALAILESERASNLEUGLN
6   THRTHRPROALASERASNPROLYSVALMET
7   ILEARGVALPHEILEVALVALLYSGLUGLY
8   GLUASPPROTHRSERLEUVALPHEHISPHE
9   THRGLYTHRPROASNALAARGGLUASNCYS
10   ASPMETILETHRASNGLULEUARGASNALA
11   ILEGLNARGGLNARGGLUGLYSERGLNSER
12   LYS

Samples:

sample_1: TFIIH Tfb1, [U-15N], 0.9 mM; potassium phosphate 20 mM; d-DTT, [U-2H], 5 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: TFIIH Tfb1, [U-13C; U-15N], 0.9 mM; potassium phosphate 20 mM; d-DTT, [U-2H], 5 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: TFIIH Tfb1, [U-13C; U-15N], 0.9 mM; potassium phosphate 20 mM; d-DTT, [U-2H], 5 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 0 mM; pH: 6.8; pressure: 1 bar; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HBHANHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HN(CO)HBsample_2isotropicsample_conditions_1
3D HNHBsample_2isotropicsample_conditions_1
3D HN(CO)CGsample_2isotropicsample_conditions_1
3D HNCGsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_1

Software:

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

MAGRO, Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, Yokoyama - peak picking

MAGRO, Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, Yokoyama - chemical shift assignment

NMRViewJ, Johnson, Blevins - peak picking

NMRViewJ, Johnson, Blevins - chemical shift assignment

NMR spectrometers:

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

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