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Found 1 Document (5.788 seconds)

BMRB: 11594

2RVB

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

Authors

Okuda, M., Nishimura, Y.

Assembly

The Acidic String of the Nucleotide Excision Repair Factor XPC

Entity

1. XPC acidic domain (polymer, Thiol state: all free), 52 monomers, 5918.105 Da Detail

GSHMAHHLKR GATMNEDSNE EEEESENDWE EVEELSEPVL GDVRESTAFS RS

2. TFIIH p62 PH domain (polymer, Thiol state: all free), 110 monomers, 12428.26 Da Detail

GSMATSSEEV LLIVKKVRQK KQDGALYLMA ERIAWAPEGK DRFTISHMYA DIKCQKISPE GKAKIQLQLV LHAGDTTNFH FSNESTAVKE RDAVKDLLQQ LLPKFKRKAN

Total weight

18346.365 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: 43.8 %, Completeness: 31.8 %, Completeness (bb): 37.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	31.8 % (600 of 1886)	29.1 % (288 of 989)	33.1 % (240 of 724)	41.6 % (72 of 173)
Backbone	37.8 % (364 of 964)	36.9 % (121 of 328)	36.6 % (175 of 478)	43.0 % (68 of 158)
Sidechain	27.2 % (293 of 1076)	25.4 % (168 of 661)	30.3 % (121 of 400)	26.7 % (4 of 15)
Aromatic	28.1 % (32 of 114)	28.1 % (16 of 57)	27.3 % (15 of 55)	50.0 % (1 of 2)
Methyl	25.3 % (40 of 158)	24.1 % (19 of 79)	26.6 % (21 of 79)

1. XPC acidic domain

GSHMAHHLKR GATMNEDSNE EEEESENDWE EVEELSEPVL GDVRESTAFS RS

2. TFIIH p62 PH domain

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

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
9	potassium phosphate	natural abundance	buffer	20 mM
10	DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	10 %

Chem. Shift Complete2

Sequence coverage: 73.5 %, Completeness: 51.2 %, Completeness (bb): 54.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	51.2 % (1932 of 3772)	49.0 % (969 of 1978)	53.0 % (768 of 1448)	56.4 % (195 of 346)
Backbone	54.0 % (1042 of 1928)	52.1 % (342 of 656)	54.4 % (520 of 956)	57.0 % (180 of 316)
Sidechain	49.3 % (1060 of 2152)	47.6 % (629 of 1322)	52.0 % (416 of 800)	50.0 % (15 of 30)
Aromatic	40.4 % (92 of 228)	41.2 % (47 of 114)	39.1 % (43 of 110)	50.0 % (2 of 4)
Methyl	52.5 % (166 of 316)	51.9 % (82 of 158)	53.2 % (84 of 158)

1. XPC acidic domain

GSHMAHHLKR GATMNEDSNE EEEESENDWE EVEELSEPVL GDVRESTAFS RS

2. TFIIH p62 PH domain

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

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
9	potassium phosphate	natural abundance	buffer	20 mM
10	DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

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

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.16 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2RVB, Strand ID: A, B Detail

Release date

2016-02-14

Citation

Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC
Okuda, M., Kinoshita, M., Kakumu, E., Sugasawa, K., Nishimura, Y.
Structure (2015), 23, 1827-1837, PubMed 26278177 , DOI 10.1016/j.str.2015.07.009 , Abstract

Related entities 1. XPC acidic domain, : 2 entities Detail

Related entities 2. TFIIH p62 PH domain, : 3 : 5 entities Detail

Interaction partners 1. XPC acidic domain, : 26 interactors Detail

More details for 26 interactors identified by 15 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
9	potassium phosphate	natural abundance	buffer	20 mM
10	DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
9	potassium phosphate	natural abundance	buffer	20 mM
10	DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	10 %

7 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
9	potassium phosphate	natural abundance	buffer	20 mM
10	DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	10 %

8 3D HNHB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
3	potassium phosphate	natural abundance	buffer	20 mM
4	DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
7	XPC acidic domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	TFIIH p62 PH domain	natural abundance	protein	0.48 mM
9	potassium phosphate	natural abundance	buffer	20 mM
10	DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	10 %

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
12	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
13	XPC acidic domain	natural abundance	protein	0.48 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	DTT	[U-2H]		5 mM
16	H2O	natural abundance	solvent	90 %
17	D2O	[U-2H]	solvent	10 %

12 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
18	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
19	XPC acidic domain	natural abundance	protein	0.48 mM
20	potassium phosphate	natural abundance	buffer	20 mM
21	DTT	[U-2H]		5 mM
22	D2O	[U-2H]	solvent	10 %

13 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
12	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
13	XPC acidic domain	natural abundance	protein	0.48 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	DTT	[U-2H]		5 mM
16	H2O	natural abundance	solvent	90 %
17	D2O	[U-2H]	solvent	10 %

14 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
12	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
13	XPC acidic domain	natural abundance	protein	0.48 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	DTT	[U-2H]		5 mM
16	H2O	natural abundance	solvent	90 %
17	D2O	[U-2H]	solvent	10 %

15 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
12	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
13	XPC acidic domain	natural abundance	protein	0.48 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	DTT	[U-2H]		5 mM
16	H2O	natural abundance	solvent	90 %
17	D2O	[U-2H]	solvent	10 %

16 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
18	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
19	XPC acidic domain	natural abundance	protein	0.48 mM
20	potassium phosphate	natural abundance	buffer	20 mM
21	DTT	[U-2H]		5 mM
22	D2O	[U-2H]	solvent	10 %

17 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
18	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
19	XPC acidic domain	natural abundance	protein	0.48 mM
20	potassium phosphate	natural abundance	buffer	20 mM
21	DTT	[U-2H]		5 mM
22	D2O	[U-2H]	solvent	10 %

18 3D HNHB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
12	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
13	XPC acidic domain	natural abundance	protein	0.48 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	DTT	[U-2H]		5 mM
16	H2O	natural abundance	solvent	90 %
17	D2O	[U-2H]	solvent	10 %

19 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
12	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
13	XPC acidic domain	natural abundance	protein	0.48 mM
14	potassium phosphate	natural abundance	buffer	20 mM
15	DTT	[U-2H]		5 mM
16	H2O	natural abundance	solvent	90 %
17	D2O	[U-2H]	solvent	10 %

20 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 305 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
18	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
19	XPC acidic domain	natural abundance	protein	0.48 mM
20	potassium phosphate	natural abundance	buffer	20 mM
21	DTT	[U-2H]		5 mM
22	D2O	[U-2H]	solvent	10 %

nullKeywords PROTEIN COMPLEX

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Found 1 Document (5.788 seconds)

BMRB: 11594

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. XPC acidic domain, : 2 entities Detail

Related entities 2. TFIIH p62 PH domain, : 3 : 5 entities Detail

Interaction partners 1. XPC acidic domain, : 26 interactors Detail

Experiments performed 20 experiments Detail

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