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BMRB: 15877

2K6Q

LC3 p62 complex structure

Authors

Noda, N., Kumeta, H., Nakatogawa, H., Satoo, K., Adachi, W., Ishii, J., Fujioka, Y., Ohsumi, Y., Inagaki, F.

Assembly

LC3/p62 complex

Entity

1. LC3 (polymer, Thiol state: not present), 121 monomers, 14230.17 Da Detail

SMPSEKTFKQ RRSFEQRVED VRLIREQHPT KIPVIIERYK GEKQLPVLDK TKFLVPDHVN MSELIKIIRR RLQLNANQAF FLLVNGHSMV SVSTPISEVY ESERDEDGFL YMVYASQETF G

2. p62 peptide (polymer, Thiol state: not present), 17 monomers, 1878.925 Da Detail

MSGGDDDWTH LSSKEVD

Total weight

16109.095 Da

Max. entity weight

14230.17 Da

Source organism

Rattus norvegicus

Exptl. method

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.4 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.4 % (1591 of 1668)	96.6 % (846 of 876)	92.9 % (602 of 648)	99.3 % (143 of 144)
Backbone	97.7 % (797 of 816)	98.2 % (271 of 276)	96.8 % (395 of 408)	99.2 % (131 of 132)
Sidechain	93.8 % (923 of 984)	95.8 % (575 of 600)	90.3 % (336 of 372)	100.0 % (12 of 12)
Aromatic	75.4 % (98 of 130)	93.8 % (61 of 65)	56.3 % (36 of 64)	100.0 % (1 of 1)
Methyl	98.6 % (140 of 142)	97.2 % (69 of 71)	100.0 % (71 of 71)

1. LC3

SMPSEKTFKQ RRSFEQRVED VRLIREQHPT KIPVIIERYK GEKQLPVLDK TKFLVPDHVN MSELIKIIRR RLQLNANQAF FLLVNGHSMV SVSTPISEVY ESERDEDGFL YMVYASQETF G

2. p62 peptide

MSGGDDDWTH LSSKEVD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2K6Q, Strand ID: A, B Detail

Release date

2008-11-25

Citation

Structural basis of target recognition by Atg8/LC3 during selective autophagy
Noda, N.N., Kumeta, H., Nakatogawa, H., Satoo, K., Adachi, W., Ishii, J., Fujioka, Y., Ohsumi, Y., Inagaki, F.
Genes. Cells. (2008), 13, 1211-1218, PubMed 19021777 , DOI 10.1111/j.1365-2443.2008.01238.x , Abstract

Related entities 1. LC3, : 3 : 78 entities Detail

Related entities 2. p62 peptide, : 1 : 7 entities Detail

Interaction partners 2. p62 peptide, : 29 interactors Detail

More details for 29 interactors identified by 16 citations

Experiments performed 22 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

3 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

4 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

6 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

7 3D HN(CA)HA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

8 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

9 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

10 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

11 3D CCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

12 2D HbCbCgCdHd

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

13 2D HbCbHcCdCeHe

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	LC3	[U-99% 13C; U-99% 15N]		0.8 mM
2	p62 peptide	natural abundance		1.2 mM
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	H2O	natural abundance		90 %
6	D2O	[U-100% 2H]		10 %

14 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

15 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

16 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

17 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

18 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

19 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

20 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

21 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

22 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	p62 peptide	[U-99% 13C; U-99% 15N]		0.8 mM
8	LC3	natural abundance		1.2 mM
9	sodium phosphate	natural abundance		25 mM
10	sodium chloride	natural abundance		100 mM
11	H2O	natural abundance		90 %
12	D2O	[U-100% 2H]		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15877_2k6q.nef
Input source #2: Coordindates	2k6q.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-------10
SMPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVY
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------110-------120
ESERDEDGFLYMVYASQETFG
|||||||||||||||||||||
ESERDEDGFLYMVYASQETFG
-------110-------120-

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

-------340-------
MSGGDDDWTHLSSKEVD
|||||||||||||||||
MSGGDDDWTHLSSKEVD
--------10-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	121	0	0	100.0
B	B	17	0	0	100.0

Content subtype: combined_15877_2k6q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1626		100.0 (chain: A, length: 121), 100.0 (chain: B, length: 17)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	4524 (1)	noe	98.3 (chain: A, length: 121), 94.1 (chain: B, length: 17)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	137 (137)	.	82.6 (chain: A, length: 121)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 100.0%

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
SMPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVY

0-------110-------120
ESERDEDGFLYMVYASQETFG
|||||||||||||||||||||
ESERDEDGFLYMVYASQETFG

Entity_assembly_ID: B, Chain length: 17, Sequence coverage: 100.0%

-------340-------
MSGGDDDWTHLSSKEVD
|||||||||||||||||
MSGGDDDWTHLSSKEVD

Total number of assignments
- ¹H chemical shifts: 859
- ¹³C chemical shifts: 621
- ¹⁵N chemical shifts: 146

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	GLN	CD	180.418
15	GLN	CD	180.506
21	ARG	CZ	175.501
24	ARG	CZ	175.778
26	GLN	CD	179.627
37	ARG	CZ	175.847
43	GLN	CD	180.024
59	ASN	CG	175.725
69	ARG	CZ	175.209
72	GLN	CD	181.421
74	ASN	CG	176.348
76	ASN	CG	177.281
77	GLN	CD	179.926
84	ASN	CG	178.387
116	GLN	CD	180.566

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	787	771	98.0
¹³C chemical shifts	580	541	93.3
¹⁵N chemical shifts	136	129	94.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	240	238	99.2
¹³C chemical shifts	242	234	96.7
¹⁵N chemical shifts	115	114	99.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	547	533	97.4
¹³C chemical shifts	338	307	90.8
¹⁵N chemical shifts	21	15	71.4

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	70	100.0
¹³C chemical shifts	70	70	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	51	89.5
¹³C chemical shifts	57	29	50.9

Entity_assemble_ID: B

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
- Chain_ID: B

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 121, Sequence coverage: 98.3%
  - Entity_assembly_ID: B, Chain length: 17, Sequence coverage: 94.1%
- Total number of restraints: 4524
- Weight of restraints: 1.0 (4524)
- Potential type of restraints: upper-bound-parabolic (4524)
- Range of distance target values: 2.22, 6.12 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 121, Sequence coverage: 82.6%
- Total number of restraints: 137
- Total number of restraints per polymer type: 137
- Weight of restraints: 1.0 (137)
- Potential type of restraints: square-well-parabolic (137)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords LC3, p62