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BMRB: 25719

2N5K

Regnase-1 Zinc finger domain

Authors

Yokogawa, M., Tsushima, T., Noda, N.N., Kumeta, H., Adachi, W., Enokizono, Y., Yamashita, K., Standley, D.M., Takeuchi, O., Akira, S., Inagaki, F.

Assembly

Regnase-1 Zinc finger domain

Entity

1. Regnase-1 Zinc finger domain, entity 1 (polymer, Thiol state: all other bound), 29 monomers, 3480.996 Da Detail

SEHRKQPCPY GKKCTYGIKC RFFHPERPS

2. ZINC ION (non-polymer), 65.409 Da

Total weight

3546.405 Da

Max. entity weight

3480.996 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS8:SG	2:ZN1:ZN
2	na	sing	1:CYS14:SG	2:ZN1:ZN
3	na	sing	1:CYS20:SG	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

distance geometry, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.1 %, Completeness (bb): 82.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (328 of 364)	95.5 % (189 of 198)	80.7 % (113 of 140)	100.0 % (26 of 26)
Backbone	82.5 % (137 of 166)	96.4 % (54 of 56)	68.2 % (58 of 85)	100.0 % (25 of 25)
Sidechain	96.9 % (218 of 225)	95.1 % (135 of 142)	100.0 % (82 of 82)	100.0 % (1 of 1)
Aromatic	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (22 of 22)
Methyl	100.0 % (6 of 6)	100.0 % (3 of 3)	100.0 % (3 of 3)

1. entity 1

SEHRKQPCPY GKKCTYGIKC RFFHPERPS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

Protein Blocks Logo

Calculated from 20 models in PDB: 2N5K, Strand ID: A Detail

Release date

2016-03-13

Citation

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Yokogawa, M., Tsushima, T., Noda, N.N., Kumeta, H., Adachi, W., Enokizono, Y., Yamashita, K., Standley, D.M., Takeuchi, O., Akira, S., Inagaki, F.
Sci. Rep. (2016), 6, 22324-22324, PubMed 26927947 , DOI 10.1038/srep22324 , Abstract

Related entities 1. Regnase-1 Zinc finger domain, entity 1, : 1 : 4 : 2 : 22 entities Detail

Interaction partners 1. Regnase-1 Zinc finger domain, entity 1, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

2 2D 1H-13C HSQC aliphatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

3 2D 1H-13C HSQC aromatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

4 3D HNCACB

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

5 3D C(CO)NH

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

6 3D CBCA(CO)NH

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

7 3D HBHA(CO)NH

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

8 3D (HCA)CO(CA)NH

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

9 3D HNCA

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

10 3D HN(CA)HA

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

11 3D HN(CO)CA

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

12 3D HNCO

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

13 2D HbCbCgCdHd

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

14 2D HbCbCgCdCeHe

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

15 3D HCCH-TOCSY aliphatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

16 3D HCCH-TOCSY aromatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

17 3D 1H-13C NOESY aliphatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

18 3D 1H-15N NOESY

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

19 3D 1H-13C NOESY aromatic

Instrument

Agilent INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Reg1_ZnF	[U-99% 13C; U-99% 15N]	protein	1.3 mM
2	D2O	[U-2H]	solvent	10 % v/v
3	DSS	natural abundance		5 ug
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25719_2n5k.nef
Input source #2: Coordindates	2n5k.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:306:CYS:SG	A:318:CYS:SG	reduced, CA 57.591, CB 30.81 ppm	reduced, CA 61.962, CB 30.054 ppm	2.611

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:24:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:20:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:14:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:8:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

-300-----310-------320-------
SEHRKQPCPYGKKCTYGIKCRFFHPERPS
|||||||||||||||||||||||||||||
SEHRKQPCPYGKKCTYGIKCRFFHPERPS
--------10--------20---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	29	0	0	100.0

Content subtype: combined_25719_2n5k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	332		100.0 (chain: A, length: 29)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	463 (1)	noe	96.6 (chain: A, length: 29)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	18 (18)	.	69.0 (chain: A, length: 29)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 195
  - ¹³C chemical shifts: 111
  - ¹⁵N chemical shifts: 26
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 96.6%
- Total number of restraints: 463
- Weight of restraints: 1.0 (463)
- Potential type of restraints: upper-bound-parabolic (463)
- Range of distance target values: 2.24, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 69.0%
- Total number of restraints: 18
- Total number of restraints per polymer type: 18
- Weight of restraints: 1.0 (18)
- Potential type of restraints: square-well-parabolic (18)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Regnase, Regnase-1, Zc3h12a, Zinc finger