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BMRB: 16835

2KWC

The NMR structure of the autophagy-related protein Atg8

Authors

Kumeta, H., Watanabe, M., Nakatogawa, H., Yamaguchi, M., Ogura, K., Adachi, W., Fujioka, Y., Noda, N.N., Ohsumi, Y., Inagaki, F.

Assembly

Atg8

Entity

1. Atg8 (polymer, Thiol state: not present), 116 monomers, 13439.38 Da Detail

MKSTFKSEYP FEKRKAESER IADRFPNRIP VICEKAEKSD IPEIDKRKYL VPADLTVGQF VYVIRKRIML PPEKAIFIFV NDTLPPTAAL MSAIYQEHKD KDGFLYVTYS GENTFG

Formula weight

13439.38 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.7 %, Completeness (bb): 98.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.7 % (1379 of 1426)	98.4 % (738 of 750)	93.8 % (529 of 564)	100.0 % (112 of 112)
Backbone	98.2 % (666 of 678)	99.1 % (225 of 227)	97.1 % (334 of 344)	100.0 % (107 of 107)
Sidechain	95.9 % (825 of 860)	98.1 % (513 of 523)	92.5 % (307 of 332)	100.0 % (5 of 5)
Aromatic	78.8 % (104 of 132)	95.5 % (63 of 66)	62.1 % (41 of 66)
Methyl	100.0 % (120 of 120)	100.0 % (60 of 60)	100.0 % (60 of 60)

1. Atg8 K26P

MKSTFKSEYP FEKRKAESER IADRFPNRIP VICEKAEKSD IPEIDKRKYL VPADLTVGQF VYVIRKRIML PPEKAIFIFV NDTLPPTAAL MSAIYQEHKD KDGFLYVTYS GENTFG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.21 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2010-05-10

Citation

The NMR structure of the autophagy-related protein Atg8
Kumeta, H., Watanabe, M., Nakatogawa, H., Yamaguchi, M., Ogura, K., Adachi, W., Fujioka, Y., Noda, N.N., Ohsumi, Y., Inagaki, F.
J. Biomol. NMR (2010), 47, 237-241, PubMed 20428927 , DOI 10.1007/s10858-010-9420-1 , Abstract

Related entities 1. Atg8, : 1 : 7 : 6 : 232 entities Detail

Interaction partners 1. Atg8, : 27 interactors Detail

More details for 27 interactors identified by 15 citations

Experiments performed 14 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 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D HN(CA)HA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

10 3D CCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

11 2D HbCbCgCdHd

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

12 2D HbCbCgCdCeHe

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

13 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

14 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 297 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Atg8 K26P	[U-99% 13C; U-99% 15N]		0.6 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16835_2kwc.nef
Input source #2: Coordindates	2kwc.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MKSTFKSEYPFEKRKAESERIADRFPNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKSTFKSEYPFEKRKAESERIADRFPNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKD

-------110------
KDGFLYVTYSGENTFG
||||||||||||||||
KDGFLYVTYSGENTFG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	116	0	0	100.0

Content subtype: combined_16835_2kwc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1371		100.0 (chain: A, length: 116)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3176 (1)	noe	100.0 (chain: A, length: 116)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 116, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 737
  - ¹³C chemical shifts: 521
  - ¹⁵N chemical shifts: 113
- 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: 116, Sequence coverage: 100.0%
- Total number of restraints: 3176
- Weight of restraints: 1.0 (3176)
- Potential type of restraints: upper-bound-parabolic (3176)
- Range of distance target values: 2.26, 6.81 (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 Atg8, Autophagy