BMRBj - BMREntryMaster

Found 1 Document (6.043 seconds)

BMRB: 11578

2RUK

Solution structure of the complex between p53 transactivation domain 2 and TFIIH p62 PH domain

Authors

Okuda, M., Nishimura, Y.

Assembly

complex between p53 transactivation domain 2 and TFIIH p62 PH domain

Entity

1. p53 TAD2 (polymer, Thiol state: not present), 22 monomers, 2724.600 Da Detail

DDLMLXPDDI EQWFXEDPGP DE

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

15152.859 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: 37.1 %, Completeness: 20.5 %, Completeness (bb): 23.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	20.5 % (319 of 1554)	25.2 % (206 of 817)	13.8 % (83 of 600)	21.9 % (30 of 137)
Backbone	23.0 % (177 of 768)	32.3 % (84 of 260)	16.4 % (63 of 384)	24.2 % (30 of 124)
Sidechain	18.0 % (164 of 910)	22.1 % (123 of 557)	12.1 % (41 of 340)	0.0 % (0 of 13)
Aromatic	8.8 % (9 of 102)	17.6 % (9 of 51)	0.0 % (0 of 49)	0.0 % (0 of 2)
Methyl	19.1 % (26 of 136)	25.0 % (17 of 68)	13.2 % (9 of 68)

1. p53 TAD2

DDLMLXPDDI EQWFXEDPGP DE

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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

Chem. Shift Complete2

Sequence coverage: 82.6 %, Completeness: 51.3 %, Completeness (bb): 53.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	51.3 % (1595 of 3108)	52.8 % (862 of 1634)	48.8 % (586 of 1200)	53.6 % (147 of 274)
Backbone	53.1 % (815 of 1536)	57.1 % (297 of 520)	49.7 % (382 of 768)	54.8 % (136 of 248)
Sidechain	49.9 % (908 of 1820)	50.8 % (566 of 1114)	48.7 % (331 of 680)	42.3 % (11 of 26)
Aromatic	42.2 % (86 of 204)	47.1 % (48 of 102)	37.8 % (37 of 98)	25.0 % (1 of 4)
Methyl	56.6 % (154 of 272)	59.6 % (81 of 136)	53.7 % (73 of 136)

1. p53 TAD2

DDLMLXPDDI EQWFXEDPGP DE

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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

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: -0.1 ppm, Outliers: 3 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: -0.1 ppm, Outliers: 3 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: -0.09 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: 0.19 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-09-30

Citation

Extended string binding mode of the phosphorylated transactivation domain of tumor suppressor p53
Okuda, M., Nishimura, Y.
J. Am. Chem. Soc. (2014), 136, 14143-14152, PubMed 25216154 , DOI 10.1021/ja506351f , Abstract

Related entities 1. p53 TAD2, : 3 : 9 entities Detail

Related entities 2. TFIIH p62 PH domain, : 3 : 4 entities Detail

Interaction partners 1. p53 TAD2, : 372 interactors Detail

More details for 372 interactors identified by 177 citations

Experiments performed 14 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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 - 600 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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 - 600 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

8 3D HNHB

Instrument

Bruker Avance - 600 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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 2D 1H-1H TOCSY

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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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 2D 1H-1H 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

11 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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 %

12 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

13 2D 1H-1H 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
2	p53 TAD2	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 %

14 2D 1H-1H 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	TFIIH p62 PH domain	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	p53 TAD2	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	100 %

nullKeywords PROTEIN COMPLEX

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (6.043 seconds)

BMRB: 11578

Sample #1

Sample #2

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. p53 TAD2, : 3 : 9 entities Detail

Related entities 2. TFIIH p62 PH domain, : 3 : 4 entities Detail

Interaction partners 1. p53 TAD2, : 372 interactors Detail

Experiments performed 14 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample