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BMRB: 18916

2M2I

NMR solution structure of BRCT domain of yeast REV1

Authors

Pustovalova, Y., Maciejewski, M.W., Korzhnev, D.M.

Assembly

BRCT domain of yeast REV1

Entity

1. BRCT domain of yeast REV1 (polymer), 94 monomers, 10775.46 Da Detail

ISSQSSKIFK NCVIYINGYT KPGRLQLHEM IVLHGGKFLH YLSSKKTVTH IVASNLPLKK RIEFANYKVV SPDWIVDSVK EARLLPWQNY SLTS

Formula weight

10775.46 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.6 %, Completeness: 89.7 %, Completeness (bb): 89.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (1041 of 1161)	91.2 % (551 of 604)	88.0 % (402 of 457)	88.0 % (88 of 100)
Backbone	89.6 % (498 of 556)	90.4 % (170 of 188)	89.9 % (250 of 278)	86.7 % (78 of 90)
Sidechain	90.2 % (627 of 695)	91.6 % (381 of 416)	87.7 % (236 of 269)	100.0 % (10 of 10)
Aromatic	72.7 % (80 of 110)	87.3 % (48 of 55)	56.6 % (30 of 53)	100.0 % (2 of 2)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. entity

ISSQSSKIFK NCVIYINGYT KPGRLQLHEM IVLHGGKFLH YLSSKKTVTH IVASNLPLKK RIEFANYKVV SPDWIVDSVK EARLLPWQNY SLTS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

LACS Plot; CA

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.36 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M2I, Strand ID: A Detail

Release date

2013-01-21

Citation

NMR mapping of PCNA interaction with translesion synthesis DNA polymerase Rev1 mediated by Rev1-BRCT domain
Pustovalova, Y., Maciejewski, M.W., Korzhnev, D.M.
J. Mol. Biol. (2013), 425, 3091-3105, PubMed 23747975 , DOI 10.1016/j.jmb.2013.05.029 , Abstract

Related entities 1. BRCT domain of yeast REV1, : 1 : 2 : 3 : 139 entities Detail

Interaction partners 1. BRCT domain of yeast REV1, : 10 interactors Detail

More details for 10 interactors identified by 7 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

2 2D 1H-13C HSQC

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian VNMRS - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

4 3D HNCA

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

5 3D HN(CO)CA

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

6 3D HNCACB

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

7 3D CBCA(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

8 3D HNCO

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

9 3D C(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

10 3D HBHA(CO)NH

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

11 3D HCCH-TOCSY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

12 3D CCH-TOCSY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

13 3D HCCH-TOCSY-aro

Instrument

Varian VNMRS - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

14 3D 1H-13C NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

15 3D 1H-15N NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

16 3D 1H-13C NOESY aromatic

Instrument

Varian VNMRS - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	Rev1-BRCT	[U-99% 13C; U-99% 15N]		70 uM
2	potassium phosphate	natural abundance		50 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18916_2m2i.nef
Input source #2: Coordindates	2m2i.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----
ISSQSSKIFKNCVIYINGYTKPGRLQLHEMIVLHGGKFLHYLSSKKTVTHIVASNLPLKKRIEFANYKVVSPDWIVDSVKEARLLPWQNYSLTS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ISSQSSKIFKNCVIYINGYTKPGRLQLHEMIVLHGGKFLHYLSSKKTVTHIVASNLPLKKRIEFANYKVVSPDWIVDSVKEARLLPWQNYSLTS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	94	0	0	100.0

Content subtype: combined_18916_2m2i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1030		92.6 (chain: A, length: 94)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2367 (1)	noe	91.5 (chain: A, length: 94)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	136 (136)	.	88.3 (chain: A, length: 94)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 92.6%
- Total number of assignments
  - ¹H chemical shifts: 546
  - ¹³C chemical shifts: 398
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 91.5%
- Total number of restraints: 2352
- Weight of restraints: 1.0 (2352)
- Potential type of restraints: square-well-parabolic (2352)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 88.3%
- Total number of restraints: 136
- Total number of restraints per polymer type: 136
- Weight of restraints: 1.0 (136)
- Potential type of restraints: square-well-parabolic (136)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords BRCT, REV1