BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	84.8 % (526 of 620)	91.0 % (294 of 323)	76.3 % (180 of 236)	85.2 % (52 of 61)
Backbone	82.9 % (257 of 310)	97.2 % (103 of 106)	68.0 % (104 of 153)	98.0 % (50 of 51)
Sidechain	88.6 % (318 of 359)	88.0 % (191 of 217)	94.7 % (125 of 132)	20.0 % (2 of 10)
Aromatic	77.8 % (28 of 36)	77.8 % (14 of 18)	77.8 % (14 of 18)
Methyl	98.5 % (65 of 66)	97.0 % (32 of 33)	100.0 % (33 of 33)

1. entity

GPLGSSEDQT AALMAHLFEM GFCDRQLNLR LLKKHNYNIL QVVTELLQLN NN

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

Protein Blocks Logo

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

Release date

2014-04-06

Citation

Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin
Walinda, E., Morimoto, D., Sugase, K., Konuma, T., Tochio, H., Shirakawa, M.
J. Biol. Chem. (2014), 289, 13890-13902, PubMed 24692539 , DOI 10.1074/jbc.M114.555441 , Abstract

Related entities 1. UBA Domain of Human NBR1, : 1 : 1 : 2 : 15 entities Detail

Interaction partners 1. UBA Domain of Human NBR1, : 34 interactors Detail

More details for 34 interactors identified by 14 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

7 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

8 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

13 2D 1H-15N HSQC IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
10	potassium phosphate	natural abundance	20 mM
11	potassium chloride	natural abundance	5 mM
12	EDTA	natural abundance	1 mM
13	benzamidine	natural abundance	1 mM
14	DTT	natural abundance	1 mM
15	sodium azide	natural abundance	0.02 %
16	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	0.5 mM
17	Pf1 phage	natural abundance	12.5 mg/mL
18	sodium chloride	natural abundance	150 mM
19	H2O	natural abundance	95 %
20	D2O	natural abundance	5 %

14 2D 1H-15N HSQC IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Sample used for NMR-double and triple resonance experiments

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	20 mM
2	potassium chloride	natural abundance	5 mM
3	EDTA	natural abundance	1 mM
4	benzamidine	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	sodium azide	natural abundance	0.02 %
7	NBR1 residues 913-959	[U-100% 13C; U-100% 15N]	1.2 mM
8	H2O	natural abundance	95 %
9	D2O	natural abundance	5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19606_2mgw.nef
Input source #2: Coordindates	2mgw.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

--910-----920-------930-------940-------950---------
GPLGSSEDQTAALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQLNNN
||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSSEDQTAALMAHLFEMGFCDRQLNLRLLKKHNYNILQVVTELLQLNNN
--------10--------20--------30--------40--------50--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	52	0	0	100.0

Content subtype: combined_19606_2mgw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	516		98.1 (chain: A, length: 52)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1385 (1)	noe	92.3 (chain: A, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 98.1%
- Total number of assignments
  - ¹H chemical shifts: 290
  - ¹³C chemical shifts: 176
  - ¹⁵N chemical shifts: 50
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	290	89.8
¹³C chemical shifts	236	176	74.6
¹⁵N chemical shifts	63	50	79.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	106	103	97.2
¹³C chemical shifts	104	51	49.0
¹⁵N chemical shifts	51	50	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	217	187	86.2
¹³C chemical shifts	132	125	94.7
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	33	94.3
¹³C chemical shifts	35	33	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	14	77.8
¹³C chemical shifts	18	14	77.8

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 92.3%
- Total number of restraints: 1382
- Weight of restraints: 1.0 (1382)
- Potential type of restraints: upper-bound-parabolic (1382)
- Range of distance target values: 2.53, 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

Keywords autophagy, protein degradation, ubiquitin binding

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Found 1 Document (1.474 seconds)

BMRB: 19606

Sample

Related entities 1. UBA Domain of Human NBR1, : 1 : 1 : 2 : 15 entities Detail

Interaction partners 1. UBA Domain of Human NBR1, : 34 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 3 contents Detail