BMRBj - BMREntryMaster

Found 1 Document (0.602 seconds)

BMRB: 36405

7DTH

Solution structure of RPB6, common subunit of RNA polymerases I, II, and III

Authors

Okuda, M., Nishimura, Y.

Assembly

DP1, General transcription factor IIH subunit 1

Entity

1. DP1, General transcription factor IIH subunit 1 (polymer, Thiol state: all free), 130 monomers, 14759.18 Da Detail

GSHMSDNEDN FDGDDFDDVE EDEGLDDLEN AEEEGQENVE ILPSGERPQA NQKRITTPYM TKYERARVLG TRALQIAMCA PVMVELEGET DPLLIAMKEL KARKIPIIIR RYLPDGSYED WGVDELIITD

Formula weight

14759.18 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, heteronucl_NOEs

Chem. Shift Complete

Sequence coverage: 97.7 %, Completeness: 92.3 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (1372 of 1487)	88.9 % (688 of 774)	95.8 % (548 of 572)	96.5 % (136 of 141)
Backbone	96.6 % (740 of 766)	94.3 % (247 of 262)	97.9 % (373 of 381)	97.6 % (120 of 123)
Sidechain	89.2 % (751 of 842)	86.1 % (441 of 512)	94.2 % (294 of 312)	88.9 % (16 of 18)
Aromatic	58.8 % (40 of 68)	58.8 % (20 of 34)	57.6 % (19 of 33)	100.0 % (1 of 1)
Methyl	94.9 % (129 of 136)	91.2 % (62 of 68)	98.5 % (67 of 68)

1. DNA-directed RNA polymerases I, II, and III subunit RPABC2

GSHMSDNEDN FDGDDFDDVE EDEGLDDLEN AEEEGQENVE ILPSGERPQA NQKRITTPYM TKYERARVLG TRALQIAMCA PVMVELEGET DPLLIAMKEL KARKIPIIIR RYLPDGSYED WGVDELIITD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-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 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	NaCl	natural abundance	salt	25 mM
10	d-DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	100 %

Heteronucl. NOE

108 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 K, pH 6.8 Detail

Release date

2021-07-13

Citation

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit
Okuda, M., Suwa, T., Suzuki, H., Yamaguchi, Y., Nishimura, Y.
Nucleic Acids Res. (2022), 50, 1-16, PubMed 34268577 , DOI 10.1093/nar/gkab612 , Abstract

Related entities 1. DP1, General transcription factor IIH subunit 1, : 1 : 1 : 41 : 73 entities Detail

Interaction partners 1. DP1, General transcription factor IIH subunit 1, : 6 interactors Detail

More details for 6 interactors identified by 2 citations

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-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 III HD - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	NaCl	natural abundance	salt	25 mM
10	d-DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	NaCl	natural abundance	salt	25 mM
10	d-DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	100 %

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

5 3D CBCANH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

6 3D HNCO

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

7 3D HN(CA)CO

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

8 3D HBHA(CO)NH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

9 3D HBHANH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

10 3D HN(CO)HB

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

11 3D HNHB

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

12 3D HN(CO)CG

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

13 3D HNCG

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

14 3D CC(CO)NH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

15 3D HCC(CO)NH

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

16 3D HCCH-COSY

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	NaCl	natural abundance	salt	25 mM
10	d-DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	100 %

17 3D HCCH-TOCSY

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	NaCl	natural abundance	salt	25 mM
10	d-DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	100 %

18 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
2	potassium phosphate	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	25 mM
4	d-DTT	[U-2H]		5 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

19 3D 1H-13C NOESY

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 2.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	RPB6	[U-100% 13C; U-100% 15N]	protein	2.0 mM
8	potassium phosphate	natural abundance	buffer	20 mM
9	NaCl	natural abundance	salt	25 mM
10	d-DTT	[U-2H]		5 mM
11	D2O	[U-2H]	solvent	100 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl NOE exptl data	bmr36405_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr36405_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1509		97.7 (chain: 1, length: 130)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 130, Sequence coverage: 97.7%
- Total number of assignments
  - ¹H chemical shifts: 825
  - ¹³C chemical shifts: 548
  - ¹⁵N chemical shifts: 136
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	774	691	89.3
¹³C chemical shifts	572	548	95.8
¹⁵N chemical shifts	141	136	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	262	251	95.8
¹³C chemical shifts	260	254	97.7
¹⁵N chemical shifts	123	120	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	512	440	85.9
¹³C chemical shifts	312	294	94.2
¹⁵N chemical shifts	18	16	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	67	91.8
¹³C chemical shifts	73	71	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	20	58.8
¹³C chemical shifts	33	19	57.6
¹⁵N chemical shifts	1	1	100.0

Keywords NUCLEAR PROTEIN, RNA polymerase

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Found 1 Document (0.602 seconds)

BMRB: 36405

Sample #1

Sample #2

Related entities 1. DP1, General transcription factor IIH subunit 1, : 1 : 1 : 41 : 73 entities Detail

Interaction partners 1. DP1, General transcription factor IIH subunit 1, : 6 interactors Detail

Experiments performed 19 experiments Detail

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Chemical shift validation 3 contents Detail