BMRB Entry 17879

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17879
MolProbity Validation Chart

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Title:
NMR structure of Atg8-Atg7C30 complex
Deposition date:
2011-08-23
Original release date:
2011-12-02
Authors:
Kumeta, Hiroyuki; Satoo, Kenji; Noda, Nobuo; Fujioka, Yuko; Ogura, Kenji; Nakatogawa, Hitoshi; Ohsumi, Yoshinori; Inagaki, Fuyuhiko
Citation:

Citation: Noda, Nobuo; Satoo, Kenji; Fujioka, Yuko; Kumeta, Hiroyuki; Ogura, Kenji; Nakatogawa, Hitoshi; Ohsumi, Yoshinori; Inagaki, Fuyuhiko. "Structural basis of Atg8 activation and transfer to Atg3 by a homodimeric E1, Atg7"  Mol. Cell 44, 462-475 (2011).
PubMed: 22055191

Assembly members:

Assembly members:
Atg8K26P, polymer, 117 residues, 13597.823 Da.
ATG7C30, polymer, 34 residues, 3848.176 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Aspergillus niger   Vector: pGEX6p

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Atg8K26P: HMKSTFKSEYPFEKRKAESE RIADRFPNRIPVICEKAEKS DIPEIDKRKYLVPADLTVGQ FVYVIRKRIMLPPEKAIFIF VNDTLPPTAALMSAIYQEHK DKDGFLYVTYSGENTFG
ATG7C30: GPHMISGLSVIKQEVERLGN DVFEWEDDESDEIA

Data sets:
Data typeCount
13C chemical shifts681
15N chemical shifts154
1H chemical shifts1111

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Atg8K26P1
2ATG7C302

Entities:

Entity 1, Atg8K26P 117 residues - 13597.823 Da.

1   HISMETLYSSERTHRPHELYSSERGLUTYR
2   PROPHEGLULYSARGLYSALAGLUSERGLU
3   ARGILEALAASPARGPHEPROASNARGILE
4   PROVALILECYSGLULYSALAGLULYSSER
5   ASPILEPROGLUILEASPLYSARGLYSTYR
6   LEUVALPROALAASPLEUTHRVALGLYGLN
7   PHEVALTYRVALILEARGLYSARGILEMET
8   LEUPROPROGLULYSALAILEPHEILEPHE
9   VALASNASPTHRLEUPROPROTHRALAALA
10   LEUMETSERALAILETYRGLNGLUHISLYS
11   ASPLYSASPGLYPHELEUTYRVALTHRTYR
12   SERGLYGLUASNTHRPHEGLY

Entity 2, ATG7C30 34 residues - 3848.176 Da.

1   GLYPROHISMETILESERGLYLEUSERVAL
2   ILELYSGLNGLUVALGLUARGLEUGLYASN
3   ASPVALPHEGLUTRPGLUASPASPGLUSER
4   ASPGLUILEALA

Samples:

13C_15N_Atg8K26P: Atg8K26P, [U-99% 13C; U-99% 15N], 0.8 mM; ATG7C30 2.0 mM; sodium phosphate 20 mM; sodium chloride 150 mM; DTT 5 mM; DSS 5 ug; sodium azide 0.02%; H2O 90%; D2O 10%

13C_15N_Atg7C30: ATG7C30, [U-99% 13C; U-99% 15N], 0.5 mM; Atg8K26P 1.25 mM; sodium phosphate 20 mM; sodium chloride 150 mM; DTT 5 mM; DSS 5 ug; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 170 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC13C_15N_Atg8K26Pisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic13C_15N_Atg8K26Pisotropicsample_conditions_1
3D 1H-15N NOESY13C_15N_Atg8K26Pisotropicsample_conditions_1
3D 1H-13C NOESY aliphatic13C_15N_Atg8K26Pisotropicsample_conditions_1
3D HCCH-TOCSY aliphatic13C_15N_Atg8K26Pisotropicsample_conditions_1
2D HbCbCgCdHd13C_15N_Atg8K26Pisotropicsample_conditions_1
2D 1H-13C HSQC aromatic13C_15N_Atg8K26Pisotropicsample_conditions_1
3D HNCA13C_15N_Atg8K26Pisotropicsample_conditions_1
3D HNCO13C_15N_Atg8K26Pisotropicsample_conditions_1
3D 1H-13C NOESY aromatic13C_15N_Atg8K26Pisotropicsample_conditions_1
3D CBCA(CO)NH13C_15N_Atg8K26Pisotropicsample_conditions_1
2D 1H-15N HSQC13C_15N_Atg7C30isotropicsample_conditions_1
3D HNCO13C_15N_Atg7C30isotropicsample_conditions_1
3D HNCACB13C_15N_Atg7C30isotropicsample_conditions_1
3D HNCACB13C_15N_Atg7C30isotropicsample_conditions_1
3D 1H-15N NOESY13C_15N_Atg7C30isotropicsample_conditions_1
3D C(CO)NH13C_15N_Atg7C30isotropicsample_conditions_1
2D 1H-13C HSQC aliphatic13C_15N_Atg7C30isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic13C_15N_Atg7C30isotropicsample_conditions_1
2D 1H-13C HSQC aromatic13C_15N_Atg7C30isotropicsample_conditions_1
3D HCCH-TOCSY aliphatic13C_15N_Atg7C30isotropicsample_conditions_1
3D HCCH-TOCSY aromatic13C_15N_Atg8K26Pisotropicsample_conditions_1
3D 1H-13C NOESY aromatic13C_15N_Atg7C30isotropicsample_conditions_1

Software:

VNMR v6.1C, Varian - collection

NMRPipe v5.2, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.113, Goddard - chemical shift assignment, peak picking, refinement

TALOS+ v1.01, Chen, Cornilescu, Delaglio, Bax - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz

Related Database Links:

BMRB 16120 16835
PDB
DBJ GAA21477 BAA33474
EMBL CAA56032 CAA84899 CAY77706
GB AAT92889 AHY74413 AJP37015 AJP81917 AJP82297 AAB68016 EIW10078 EWH18191
REF NP_009475 NP_012041
SP A6ZKM4 P38182 P38862
TPG DAA07045 DAA06864
AlphaFold A6ZKM4 P38182 P38862

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks