BMRBj - BMREntryMaster

Found 1 Document (1.609 seconds)

BMRB: 18842

2M14

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4

Authors

Lafrance-Vanasse, J., Arseneault, G., Cappadocia, L., Legault, P., Omichinski, J.G.

Assembly

complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4

Entity

1. Tfb1 (polymer, Thiol state: not present), 119 monomers, 13228.85 Da Detail

PSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMFS FNNRTVMDNI KMTLQQIISR YKDADGNSS

2. Rad4 (polymer, Thiol state: not present), 42 monomers, 4597.551 Da Detail

GSTDDSVEEI QSSEEDYDSE EFEDVTDGNE VAGVEDISVE IK

Total weight

17826.4 Da

Max. entity weight

13228.85 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.9 %, Completeness: 78.2 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.2 % (1409 of 1801)	76.8 % (720 of 937)	78.8 % (547 of 694)	83.5 % (142 of 170)
Backbone	80.9 % (773 of 956)	80.4 % (262 of 326)	80.6 % (382 of 474)	82.7 % (129 of 156)
Sidechain	75.9 % (757 of 997)	75.0 % (458 of 611)	76.9 % (286 of 372)	92.9 % (13 of 14)
Aromatic	92.5 % (74 of 80)	95.0 % (38 of 40)	89.7 % (35 of 39)	100.0 % (1 of 1)
Methyl	77.8 % (126 of 162)	76.5 % (62 of 81)	79.0 % (64 of 81)

1. Tfb1

PSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMFS FNNRTVMDNI KMTLQQIISR YKDADGNSS

2. Rad4

GSTDDSVEEI QSSEEDYDSE EFEDVTDGNE VAGVEDISVE IK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
2	Rad4	natural abundance	1.25 mM
3	sodium phosphate	natural abundance	20 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
7	Rad4	natural abundance	1.25 mM
8	sodium phosphate	natural abundance	20 mM
9	EDTA	natural abundance	1 mM
10	DTT	natural abundance	1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Tfb1	[U-100% 15N]	1 mM
12	Rad4	natural abundance	1.25 mM
13	sodium phosphate	natural abundance	20 mM
14	EDTA	natural abundance	1 mM
15	DTT	natural abundance	1 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
16	Tfb1	natural abundance	1.25 mM
17	Rad4	[U-100% 13C; U-100% 15N]	1 mM
18	sodium phosphate	natural abundance	20 mM
19	EDTA	natural abundance	1 mM
20	DTT	natural abundance	1 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	Tfb1	natural abundance	1.25 mM
22	Rad4	[U-100% 13C; U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	20 mM
24	EDTA	natural abundance	1 mM
25	DTT	natural abundance	1 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
26	Tfb1	natural abundance	1.25 mM
27	Rad4	[U-100% 15N]	1 mM
28	sodium phosphate	natural abundance	20 mM
29	EDTA	natural abundance	1 mM
30	DTT	natural abundance	1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M14, Strand ID: A, B Detail

Release date

2013-01-21

Citation

Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER
Lafrance-Vanasse, J., Arseneault, G., Cappadocia, L., Legault, P., Omichinski, J.G.
Nucleic Acids Res. (2013), 41, 2736-2745, PubMed 23295669 , DOI 10.1093/nar/gks1321 , Abstract

Related entities 1. Tfb1, : 2 : 4 entities Detail

Related entities 2. Rad4, : 1 : 2 : 1 entities Detail

Interaction partners 1. Tfb1, : 49 interactors Detail

More details for 49 interactors identified by 12 citations

Interaction partners 2. Rad4, : 30 interactors Detail

More details for 30 interactors identified by 7 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Tfb1	[U-100% 15N]	1 mM
12	Rad4	natural abundance	1.25 mM
13	sodium phosphate	natural abundance	20 mM
14	EDTA	natural abundance	1 mM
15	DTT	natural abundance	1 mM

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
26	Tfb1	natural abundance	1.25 mM
27	Rad4	[U-100% 15N]	1 mM
28	sodium phosphate	natural abundance	20 mM
29	EDTA	natural abundance	1 mM
30	DTT	natural abundance	1 mM

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	Tfb1	natural abundance	1.25 mM
22	Rad4	[U-100% 13C; U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	20 mM
24	EDTA	natural abundance	1 mM
25	DTT	natural abundance	1 mM

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
16	Tfb1	natural abundance	1.25 mM
17	Rad4	[U-100% 13C; U-100% 15N]	1 mM
18	sodium phosphate	natural abundance	20 mM
19	EDTA	natural abundance	1 mM
20	DTT	natural abundance	1 mM

5 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
16	Tfb1	natural abundance	1.25 mM
17	Rad4	[U-100% 13C; U-100% 15N]	1 mM
18	sodium phosphate	natural abundance	20 mM
19	EDTA	natural abundance	1 mM
20	DTT	natural abundance	1 mM

6 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
16	Tfb1	natural abundance	1.25 mM
17	Rad4	[U-100% 13C; U-100% 15N]	1 mM
18	sodium phosphate	natural abundance	20 mM
19	EDTA	natural abundance	1 mM
20	DTT	natural abundance	1 mM

7 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
16	Tfb1	natural abundance	1.25 mM
17	Rad4	[U-100% 13C; U-100% 15N]	1 mM
18	sodium phosphate	natural abundance	20 mM
19	EDTA	natural abundance	1 mM
20	DTT	natural abundance	1 mM

8 3D HCCH-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	Tfb1	natural abundance	1.25 mM
22	Rad4	[U-100% 13C; U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	20 mM
24	EDTA	natural abundance	1 mM
25	DTT	natural abundance	1 mM

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
26	Tfb1	natural abundance	1.25 mM
27	Rad4	[U-100% 15N]	1 mM
28	sodium phosphate	natural abundance	20 mM
29	EDTA	natural abundance	1 mM
30	DTT	natural abundance	1 mM

10 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	Tfb1	natural abundance	1.25 mM
22	Rad4	[U-100% 13C; U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	20 mM
24	EDTA	natural abundance	1 mM
25	DTT	natural abundance	1 mM

11 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
7	Rad4	natural abundance	1.25 mM
8	sodium phosphate	natural abundance	20 mM
9	EDTA	natural abundance	1 mM
10	DTT	natural abundance	1 mM

12 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
2	Rad4	natural abundance	1.25 mM
3	sodium phosphate	natural abundance	20 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM

13 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
2	Rad4	natural abundance	1.25 mM
3	sodium phosphate	natural abundance	20 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM

14 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
2	Rad4	natural abundance	1.25 mM
3	sodium phosphate	natural abundance	20 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM

15 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
2	Rad4	natural abundance	1.25 mM
3	sodium phosphate	natural abundance	20 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM

16 3D HCCH-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
7	Rad4	natural abundance	1.25 mM
8	sodium phosphate	natural abundance	20 mM
9	EDTA	natural abundance	1 mM
10	DTT	natural abundance	1 mM

17 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	Tfb1	[U-100% 15N]	1 mM
12	Rad4	natural abundance	1.25 mM
13	sodium phosphate	natural abundance	20 mM
14	EDTA	natural abundance	1 mM
15	DTT	natural abundance	1 mM

18 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	Tfb1	[U-100% 13C; U-100% 15N]	1 mM
7	Rad4	natural abundance	1.25 mM
8	sodium phosphate	natural abundance	20 mM
9	EDTA	natural abundance	1 mM
10	DTT	natural abundance	1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18842_2m14.nef
Input source #2: Coordindates	2m14.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNI

-------110---------
KMTLQQIISRYKDADGNSS
|||||||||||||||||||
KMTLQQIISRYKDADGNSS

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-----80--------90-------100-------110-----
GSTDDSVEEIQSSEEDYDSEEFEDVTDGNEVAGVEDISVEIK
||||||||||||||||||||||||||||||||||||||||||
GSTDDSVEEIQSSEEDYDSEEFEDVTDGNEVAGVEDISVEIK
--------10--------20--------30--------40--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0
B	B	42	0	0	100.0

Content subtype: combined_18842_2m14.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1420		100.0 (chain: A, length: 119), 35.7 (chain: B, length: 42)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2340 (1)	noe	96.6 (chain: A, length: 119), 7.1 (chain: B, length: 42)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	36 (1)	hbond	18.5 (chain: A, length: 119)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	148 (148)	.	70.6 (chain: A, length: 119), 26.2 (chain: B, length: 42)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 35.7%
- Total number of assignments
  - ¹H chemical shifts: 724
  - ¹³C chemical shifts: 552
  - ¹⁵N chemical shifts: 144
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: A
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
19	ASN	CG	176.78
49	GLN	CD	179.022
75	ASN	CG	177.095
78	ASN	CG	176.97
85	GLN	CD	180.238
92	ASN	CG	177.065
93	ASN	CG	176.424
99	ASN	CG	176.367
105	GLN	CD	178.506
106	GLN	CD	180.227
117	ASN	CG	177.343

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	718	647	90.1
¹³C chemical shifts	527	479	90.9
¹⁵N chemical shifts	132	128	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	239	237	99.2
¹³C chemical shifts	238	229	96.2
¹⁵N chemical shifts	114	113	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	479	410	85.6
¹³C chemical shifts	289	250	86.5
¹⁵N chemical shifts	18	15	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	64	95.5
¹³C chemical shifts	67	64	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	28	90.3
¹³C chemical shifts	30	25	83.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 96.6%
  - Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 7.1%
- Total number of restraints: 2338
- Weight of restraints: 1.0 (2338)
- Potential type of restraints: square-well-parabolic (2338)
- Range of distance target values: 2.3, 4.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 18.5%
  - Total number of restraints: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: square-well-parabolic (36)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 70.6%
  - Entity_assembly_ID: B, Chain length: 42, Sequence coverage: 26.2%
- Total number of restraints: 148
- Total number of restraints per polymer type: 148
- Weight of restraints: 1.0 (148)
- Potential type of restraints: square-well-parabolic (148)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PH domain, Rad4, Tfb1

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 (1.609 seconds)

BMRB: 18842

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Related entities 1. Tfb1, : 2 : 4 entities Detail

Related entities 2. Rad4, : 1 : 2 : 1 entities Detail

Interaction partners 1. Tfb1, : 49 interactors Detail

Interaction partners 2. Rad4, : 30 interactors Detail

Experiments performed 18 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail