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BMRB: 25718

2N5J

Regnase-1 N-terminal 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 N-terminal domain

Entity

1. Regnase-1 N-terminal domain (polymer, Thiol state: not present), 49 monomers, 5414.131 Da Detail

GPHMTSELQM KVDFFRKLGY SSSEIHSVLQ KLGVQADTNT VLGELVKHG

Formula weight

5414.131 Da

Source organism

Exptl. method

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.9 %, Completeness: 88.9 %, Completeness (bb): 89.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.9 % (505 of 568)	87.4 % (257 of 294)	89.2 % (198 of 222)	96.2 % (50 of 52)
Backbone	89.0 % (260 of 292)	86.3 % (88 of 102)	88.7 % (126 of 142)	95.8 % (46 of 48)
Sidechain	88.7 % (284 of 320)	88.0 % (169 of 192)	89.5 % (111 of 124)	100.0 % (4 of 4)
Aromatic	90.0 % (36 of 40)	90.0 % (18 of 20)	90.0 % (18 of 20)
Methyl	85.7 % (48 of 56)	78.6 % (22 of 28)	92.9 % (26 of 28)

1. Reg1 NTD

GPHMTSELQM KVDFFRKLGY SSSEIHSVLQ KLGVQADTNT VLGELVKHG

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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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: 2N5J, 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

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 25719 released on 2016-03-13
    Title Regnase-1 Zinc finger domain
  BMRB: 25720 released on 2016-03-13
    Title Regnase-1 C-terminal domain

Related entities 1. Regnase-1 N-terminal domain, : 1 : 4 : 31 entities Detail

Interaction partners 1. Regnase-1 N-terminal domain, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent INOVA - 800 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

2 3D 1H-13C NOESY aliphatic

Instrument

Agilent INOVA - 800 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

3 3D 1H-15N NOESY

Instrument

Agilent INOVA - 800 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 H(CCO)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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

12 2D 1H-13C HSQC aliphatic

Instrument

Agilent INOVA - 800 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
4	HEPES	natural abundance	buffer	20 mM
5	sodium chloride	natural abundance	salt	150 mM
6	H2O	natural abundance	solvent	90 % v/v

14 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_NTD	[U-99% 13C; U-99% 15N]	protein	1.1 mM
2	DSS	natural abundance		5 ug
3	D2O	[U-2H]	solvent	10 % v/v
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_25718_2n5j.nef
Input source #2: Coordindates	2n5j.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

--------50--------60--------70--------80---------
GPHMTSELQMKVDFFRKLGYSSSEIHSVLQKLGVQADTNTVLGELVKHG
|||||||||||||||||||||||||||||||||||||||||||||||||
GPHMTSELQMKVDFFRKLGYSSSEIHSVLQKLGVQADTNTVLGELVKHG
--------10--------20--------30--------40---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	49	0	0	100.0

Content subtype: combined_25718_2n5j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	542		95.9 (chain: A, length: 49)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1166 (1)	noe	93.9 (chain: A, length: 49)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	70 (70)	.	85.7 (chain: A, length: 49)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 95.9%
- Total number of assignments
  - ¹H chemical shifts: 278
  - ¹³C chemical shifts: 214
  - ¹⁵N chemical shifts: 50
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 93.9%
- Total number of restraints: 1166
- Weight of restraints: 1.0 (1166)
- Potential type of restraints: upper-bound-parabolic (1166)
- Range of distance target values: 2.31, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 49, Sequence coverage: 85.7%
- Total number of restraints: 70
- Total number of restraints per polymer type: 70
- Weight of restraints: 1.0 (70)
- Potential type of restraints: square-well-parabolic (70)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Regnase, Regnase-1, Zc3h12a