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BMRB: 34630

7OMK

The NMR structure of the Zf-GRF domains from the mouse Endonuclease VIII-LIKE 3 (mNEIL3)

Authors

Dinesh, D.C., Huskova, A., Srb, P., Veverka, V., Silhan, J.

Assembly

Endonuclease 8-like 3 (E.C.3.2.2.-,4.2.99.18)

Entity

1. Endonuclease 8-like 3 (E.C.3.2.2.-,4.2.99.18) (polymer), 93 monomers, 10798.50 Da Detail

SPLCKMHHRR CVLRVVRKDG ENKGRQFYAC SLPRGAQCGF FEWADLSFPF CKHGKRSIMK TVLKIGPNNG KNFFVCPLEK EKQCNFFQWA ENG

Formula weight

10798.5 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.8 %, Completeness (bb): 99.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.8 % (1107 of 1155)	97.7 % (596 of 610)	93.6 % (410 of 438)	94.4 % (101 of 107)
Backbone	99.8 % (547 of 548)	100.0 % (189 of 189)	99.6 % (270 of 271)	100.0 % (88 of 88)
Sidechain	93.2 % (645 of 692)	96.7 % (407 of 421)	89.3 % (225 of 252)	68.4 % (13 of 19)
Aromatic	73.1 % (98 of 134)	86.6 % (58 of 67)	58.5 % (38 of 65)	100.0 % (2 of 2)
Methyl	100.0 % (62 of 62)	100.0 % (31 of 31)	100.0 % (31 of 31)

1. entity 1

SPLCKMHHRR CVLRVVRKDG ENKGRQFYAC SLPRGAQCGF FEWADLSFPF CKHGKRSIMK TVLKIGPNNG KNFFVCPLEK EKQCNFFQWA ENG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

Release date

2021-06-14

Citation

The NMR structure of the Zf-GRF domains from the mouse Endonuclease VIII-LIKE 3 (mNEIL3)
Dinesh, D.C., Huskova, A., Srb, P., Veverka, V., Silhan, J.

Related entities 1. Endonuclease 8-like 3 (E.C.3.2.2.-,4.2.99.18), : 1 : 2 : 22 entities Detail

Interaction partners 1. Endonuclease 8-like 3 (E.C.3.2.2.-,4.2.99.18), : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

3 3D HNCO

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

4 3D HNCACB

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

5 3D HBHA(CO)NH

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

6 3D HN(CO)CA

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

7 3D 1H-13C NOESY

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

8 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

9 3D CBCA(CO)NH

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

10 3D H(CCO)NH

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

11 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 850 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	NEIL3-GRF	[U-13C; U-15N]		250 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34630_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: bmr34630_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1163		100.0 (chain: 1, length: 93)
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: 93, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 659
  - ¹³C chemical shifts: 405
  - ¹⁵N chemical shifts: 99
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords DNA BINDING PROTEIN, DNA damage, DNA repair, NEIL3-GRF, Zinc Finger