BMRB Entry 36013

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR36013
MolProbity Validation Chart

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Title:
Solution structure of the complex between DP1 acidic region and TFIIH p62 PH domain
Deposition date:
2016-07-29
Original release date:
2017-03-01
Authors:
Okuda, M.; Nishimura, Y.
Citation:

Citation: Okuda, M.; Araki, K.; Ohtani, K.; Nishimura, Y.. "The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH"  J. Mol. Biol. 428, 4993-5006 (2016).
PubMed: 27825926

Assembly members:

Assembly members:
entity_1, polymer, 19 residues, 2279.022 Da.
entity_2, polymer, 110 residues, 12450.445 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: YVGEDDEEDDDFNENDEDD
entity_2: GSMATSSEEVLLIVKKVRQK KQDGALYLMAERIAWAPEGK DRFTISHMYADIKCQKISPE GKAKIQLQLVLHAGDTTNFH FSNESTAVKERDAVKDLLQQ LLPKFKRKAN

Data sets:
Data typeCount
13C chemical shifts557
15N chemical shifts134
1H chemical shifts855

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 19 residues - 2279.022 Da.

1   TYRVALGLYGLUASPASPGLUGLUASPASP
2   ASPPHEASNGLUASNASPGLUASPASP

Entity 2, entity_2 110 residues - 12450.445 Da.

1   GLYSERMETALATHRSERSERGLUGLUVAL
2   LEULEUILEVALLYSLYSVALARGGLNLYS
3   LYSGLNASPGLYALALEUTYRLEUMETALA
4   GLUARGILEALATRPALAPROGLUGLYLYS
5   ASPARGPHETHRILESERHISMETTYRALA
6   ASPILELYSCYSGLNLYSILESERPROGLU
7   GLYLYSALALYSILEGLNLEUGLNLEUVAL
8   LEUHISALAGLYASPTHRTHRASNPHEHIS
9   PHESERASNGLUSERTHRALAVALLYSGLU
10   ARGASPALAVALLYSASPLEULEUGLNGLN
11   LEULEUPROLYSPHELYSARGLYSALAASN

Samples:

sample_1: DP1, [U-99% 13C; U-99% 15N], 0.35 mM; TFIIH p62 0.42 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: DP1, [U-99% 13C; U-99% 15N], 0.35 mM; TFIIH p62 0.42 mM; D2O, [U-2H], 100%

sample_3: DP1 0.42 mM; TFIIH p62, [U-99% 13C; U-99% 15N], 0.35 mM; H2O 90%; D2O, [U-2H], 10%

sample_4: DP1 0.42 mM; TFIIH p62, [U-99% 13C; U-99% 15N], 0.35 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.8; pressure: 1 atm; temperature: 305 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 HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_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 aromaticsample_4isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D C(CO)NHsample_3isotropicsample_conditions_1
3D H(CCO)NHsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1

Software:

Molmol, Koradi, Billeter and Wuthrich - data analysis

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

ProcheckNMR, Laskowski and MacArthur - data analysis

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

  • Bruker AvanceIII 950 MHz
  • Bruker AvanceIII 600 MHz

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