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BMRB: 17879

2LI5

NMR structure of Atg8-Atg7C30 complex

Authors

Satoo, K., Kumeta, H., Noda, N.N., Fujioka, Y., Ogura, K., Nakatogawa, H., Ohsumi, Y., Inagaki, F.

Assembly

Atg8K26P

Entity

1. Atg8K26P (polymer), 117 monomers, 13576.52 Da Detail

HMKSTFKSEY PFEKRKAESE RIADRFPNRI PVICEKAEKS DIPEIDKRKY LVPADLTVGQ FVYVIRKRIM LPPEKAIFIF VNDTLPPTAA LMSAIYQEHK DKDGFLYVTY SGENTFG

2. ATG7C30 (polymer), 34 monomers, 3845.117 Da Detail

GPHMISGLSV IKQEVERLGN DVFEWEDDES DEIA

Total weight

17421.637 Da

Max. entity weight

13576.52 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.3 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (1752 of 1820)	97.7 % (932 of 954)	93.6 % (671 of 717)	100.0 % (149 of 149)
Backbone	98.1 % (869 of 886)	98.3 % (294 of 299)	97.3 % (434 of 446)	100.0 % (141 of 141)
Sidechain	95.3 % (1027 of 1078)	97.4 % (638 of 655)	91.8 % (381 of 415)	100.0 % (8 of 8)
Aromatic	81.5 % (132 of 162)	100.0 % (81 of 81)	62.5 % (50 of 80)	100.0 % (1 of 1)
Methyl	100.0 % (154 of 154)	100.0 % (77 of 77)	100.0 % (77 of 77)

1. Atg8K26P

HMKSTFKSEY PFEKRKAESE RIADRFPNRI PVICEKAEKS DIPEIDKRKY LVPADLTVGQ FVYVIRKRIM LPPEKAIFIF VNDTLPPTAA LMSAIYQEHK DKDGFLYVTY SGENTFG

2. ATG7C30

GPHMISGLSV IKQEVERLGN DVFEWEDDES DEIA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Atg8K26P	[U-99% 13C; U-99% 15N]	0.8 mM
2	ATG7C30	natural abundance	2.0 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	150 mM
5	DTT	natural abundance	5 mM
6	DSS	natural abundance	5 ug
7	sodium azide	natural abundance	0.02 %
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
10	ATG7C30	[U-99% 13C; U-99% 15N]	0.5 mM
11	Atg8K26P	natural abundance	1.25 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	150 mM
14	DTT	natural abundance	5 mM
15	DSS	natural abundance	5 ug
16	sodium azide	natural abundance	0.02 %
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.25 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.25 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.23 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 19 models in PDB: 2LI5, Strand ID: A, B Detail

Release date

2011-12-01

Citation

Structural basis of Atg8 activation by a homodimeric E1, Atg7
Noda, N.N., Satoo, K., Fujioka, Y., Kumeta, H., Ogura, K., Nakatogawa, H., Ohsumi, Y., Inagaki, F.
Mol. Cell (2011), 44, 462-475, PubMed 22055191 , DOI 10.1016/j.molcel.2011.08.035 , Abstract

Entries sharing articles Swiss-Prot: 3 entries Detail

  Swiss-Prot: P38862 released on 1995-02-01
    Title ATG7_YEAST Entity Ubiquitin-like modifier-activating enzyme ATG7
  Swiss-Prot: P40344 released on 1995-02-01
    Title ATG3_YEAST Entity Autophagy-related protein 3
  Swiss-Prot: P38182 released on 1994-10-01
    Title ATG8_YEAST Entity Autophagy-related protein 8

Related entities 1. Atg8K26P, : 1 : 80 entities Detail

Related entities 2. ATG7C30, : 1 : 7 : 3 entities Detail

Interaction partners 2. ATG7C30, : 10 interactors Detail

More details for 10 interactors identified by 4 citations

Experiments performed 23 experiments Detail

1 2D 1H-15N HSQC