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BMRB: 16361

2KKC

NMR structure of the p62 PB1 domain

Authors

Yokochi, M., Inagaki, F.

Assembly

p62 PB1

Entity

1. p62 PB1 (polymer, Thiol state: all free), 100 monomers, 11257.80 Da Detail

HMSLTVKAYL LGKEEAAREI RRFSFCFSPE PEAEAAAGPG PCERLLSRVA VLFPALRPGG FQAHYRAERG DLVAFSSDEE LTMAMSYVKD DIFRIYIKEK

Formula weight

11257.8 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.7 %, Completeness (bb): 81.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.7 % (1022 of 1166)	94.1 % (572 of 608)	78.2 % (362 of 463)	92.6 % (88 of 95)
Backbone	81.5 % (479 of 588)	94.5 % (189 of 200)	69.0 % (203 of 294)	92.6 % (87 of 94)
Sidechain	94.6 % (636 of 672)	93.9 % (383 of 408)	95.8 % (252 of 263)	100.0 % (1 of 1)
Aromatic	87.3 % (96 of 110)	87.3 % (48 of 55)	87.3 % (48 of 55)
Methyl	99.0 % (101 of 102)	100.0 % (51 of 51)	98.0 % (50 of 51)

1. p62 PB1

HMSLTVKAYL LGKEEAAREI RRFSFCFSPE PEAEAAAGPG PCERLLSRVA VLFPALRPGG FQAHYRAERG DLVAFSSDEE LTMAMSYVKD DIFRIYIKEK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

LACS Plot; CA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2009-06-25

Citation

The NMR structure of the p62 PB1 domain, a key protein in autophagy and NF-kappaB signaling pathway
Saio, T., Yokochi, M., Inagaki, F.
J. Biomol. NMR (2009), 45, 335-341, PubMed 19728111 , DOI 10.1007/s10858-009-9370-7 , Abstract

Related entities 1. p62 PB1, : 1 : 2 : 20 entities Detail

Interaction partners 1. p62 PB1, : 5 interactors Detail

More details for 5 interactors identified by 3 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Unity Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

2 2D 1H-13C HSQC

Instrument

Varian Unity Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

3 3D CBCA(CO)NH

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

4 3D HNCO

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

5 3D HNCA

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

6 3D HNCACB

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

7 3D HBHA(CO)NH

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

8 3D HN(CO)CA

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

9 3D HCCH-TOCSY

Instrument

Varian Unity Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

10 3D (H)CCH-TOCSY

Instrument

Varian Unity Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

11 3D HNCAHA

Instrument

Varian Unity Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

12 3D 1H-15N NOESY

Instrument

Varian Unity Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

13 3D 1H-13C NOESY

Instrument

Varian Unity Inova - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	p62 PB1	[U-99% 13C; U-99% 15N]		1 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	MES	natural abundance		20 mM
5	sodium chloride	natural abundance		50 mM
6	DTT	natural abundance		10 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16361_2kkc.nef
Input source #2: Coordindates	2kkc.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

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
GPHMSLTVKAYLLGKEEAAREIRRFSFCFSPEPEAEAAAGPGPCERLLSRVAVLFPALRPGGFQAHYRAERGDLVAFSSDEELTMAMSYVKDDIFRIYIK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPHMSLTVKAYLLGKEEAAREIRRFSFCFSPEPEAEAAAGPGPCERLLSRVAVLFPALRPGGFQAHYRAERGDLVAFSSDEELTMAMSYVKDDIFRIYIK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00
EK
||
EK
--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_16361_2kkc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1024		98.0 (chain: A, length: 102)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2915 (1)	noe	97.1 (chain: A, length: 102)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	122 (122)	.	81.4 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 584
  - ¹³C chemical shifts: 352
  - ¹⁵N chemical shifts: 88
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 97.1%
- Total number of restraints: 2860
- Weight of restraints: 1.0 (2860)
- Potential type of restraints: upper-bound-parabolic (2860)
- Range of distance target values: 2.18, 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: 102, Sequence coverage: 81.4%
- Total number of restraints: 122
- Total number of restraints per polymer type: 122
- Weight of restraints: 1.0 (122)
- Potential type of restraints: square-well-parabolic (122)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords autophagy, NF-kB signaling, p62, PB1, ubiquitin-proteasome system