BMRBj - BMREntryMaster

Found 1 Document (1.629 seconds)

BMRB: 36013

5GOW

Solution structure of the complex between DP1 acidic region and TFIIH p62 PH domain

Authors

Okuda, M., Nishimura, Y.

Assembly

DP1, General transcription factor IIH subunit 1

Entity

1. DP1, General transcription factor IIH subunit 1, entity 1 (polymer, Thiol state: not present), 19 monomers, 2279.021 Da Detail

YVGEDDEEDD DFNENDEDD

2. DP1, General transcription factor IIH subunit 1, entity 2 (polymer, Thiol state: all free), 110 monomers, 12428.26 Da Detail

GSMATSSEEV LLIVKKVRQK KQDGALYLMA ERIAWAPEGK DRFTISHMYA DIKCQKISPE GKAKIQLQLV LHAGDTTNFH FSNESTAVKE RDAVKDLLQQ LLPKFKRKAN

Total weight

14707.281 Da

Max. entity weight

12428.26 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 33.3 %, Completeness: 23.4 %, Completeness (bb): 27.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	23.4 % (355 of 1516)	22.9 % (182 of 795)	22.3 % (130 of 582)	30.9 % (43 of 139)
Backbone	27.9 % (214 of 768)	29.5 % (77 of 261)	25.5 % (97 of 381)	31.7 % (40 of 126)
Sidechain	20.1 % (175 of 871)	20.0 % (107 of 534)	20.1 % (65 of 324)	23.1 % (3 of 13)
Aromatic	18.4 % (18 of 98)	18.4 % (9 of 49)	18.8 % (9 of 48)	0.0 % (0 of 1)
Methyl	14.1 % (18 of 128)	14.1 % (9 of 64)	14.1 % (9 of 64)

1. entity 1

YVGEDDEEDD DFNENDEDD

2. entity 2

GSMATSSEEV LLIVKKVRQK KQDGALYLMA ERIAWAPEGK DRFTISHMYA DIKCQKISPE GKAKIQLQLV LHAGDTTNFH FSNESTAVKE RDAVKDLLQQ LLPKFKRKAN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
6	TFIIH p62	natural abundance	protein	0.42 mM
7	D2O	[U-2H]	solvent	100 %

Chem. Shift Complete2

Sequence coverage: 85.3 %, Completeness: 52.7 %, Completeness (bb): 56.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.7 % (1599 of 3032)	51.6 % (820 of 1590)	53.2 % (619 of 1164)	57.6 % (160 of 278)
Backbone	56.1 % (861 of 1536)	56.7 % (296 of 522)	55.0 % (419 of 762)	57.9 % (146 of 252)
Sidechain	50.3 % (876 of 1742)	49.3 % (526 of 1068)	51.9 % (336 of 648)	53.8 % (14 of 26)
Aromatic	35.7 % (70 of 196)	35.7 % (35 of 98)	35.4 % (34 of 96)	50.0 % (1 of 2)
Methyl	55.5 % (142 of 256)	55.5 % (71 of 128)	55.5 % (71 of 128)

1. entity 1

YVGEDDEEDD DFNENDEDD

2. entity 2

GSMATSSEEV LLIVKKVRQK KQDGALYLMA ERIAWAPEGK DRFTISHMYA DIKCQKISPE GKAKIQLQLV LHAGDTTNFH FSNESTAVKE RDAVKDLLQQ LLPKFKRKAN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
12	DP1	natural abundance	protein	0.42 mM
13	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
14	D2O	[U-2H]	solvent	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5GOW, Strand ID: A, B Detail

Release date

2016-11-01

Citation

The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH
Okuda, M., Araki, K., Ohtani, K., Nishimura, Y.
J. Mol. Biol. (2016), 428, 4993-5006, PubMed 27825926 , DOI 10.1016/j.jmb.2016.11.001 , Abstract

Related entities 1. DP1, General transcription factor IIH subunit 1, entity 1, : 2 entities Detail

Related entities 2. DP1, General transcription factor IIH subunit 1, entity 2, : 3 : 4 entities Detail

Interaction partners 1. DP1, General transcription factor IIH subunit 1, entity 1, : 37 interactors Detail

More details for 37 interactors identified by 11 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
6	TFIIH p62	natural abundance	protein	0.42 mM
7	D2O	[U-2H]	solvent	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
6	TFIIH p62	natural abundance	protein	0.42 mM
7	D2O	[U-2H]	solvent	100 %

4 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

5 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

6 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

7 3D C(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

8 3D H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

9 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
2	TFIIH p62	natural abundance	protein	0.42 mM
3	H2O	natural abundance	solvent	90 %
4	D2O	[U-2H]	solvent	10 %

10 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] DP1, 0.42 mM TFIIH p62, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	DP1	[U-99% 13C; U-99% 15N]	protein	0.35 mM
6	TFIIH p62	natural abundance	protein	0.42 mM
7	D2O	[U-2H]	solvent	100 %

11 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

12 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
12	DP1	natural abundance	protein	0.42 mM
13	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
14	D2O	[U-2H]	solvent	100 %

13 2D 1H-13C HSQC aromatic

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
12	DP1	natural abundance	protein	0.42 mM
13	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
14	D2O	[U-2H]	solvent	100 %

14 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

15 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

16 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

17 3D C(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

18 3D H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

19 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
8	DP1	natural abundance	protein	0.42 mM
9	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
10	H2O	natural abundance	solvent	90 %
11	D2O	[U-2H]	solvent	10 %

20 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8, Details 0.35 mM [U-99% 13C; U-99% 15N] TFIIH p62, 0.42 mM DP1, 100% D2O

#	Name	Isotope labeling	Type	Concentration
12	DP1	natural abundance	protein	0.42 mM
13	TFIIH p62	[U-99% 13C; U-99% 15N]	protein	0.35 mM
14	D2O	[U-2H]	solvent	100 %

nullKeywords Cell cycle, General transcription factor, Solution structure, TRANSCRIPTION, Transcription activation, Transcription factor

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Found 1 Document (1.629 seconds)

BMRB: 36013

Sample #1

Sample #2

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DP1, General transcription factor IIH subunit 1, entity 1, : 2 entities Detail

Related entities 2. DP1, General transcription factor IIH subunit 1, entity 2, : 3 : 4 entities Detail

Interaction partners 1. DP1, General transcription factor IIH subunit 1, entity 1, : 37 interactors Detail

Experiments performed 20 experiments Detail

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