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BMRB Entry 15877

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15877
MolProbity Validation Chart

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Title: LC3 p62 complex structure   PubMed: 19021777

Deposition date: 2008-07-17 Original release date: 2008-11-26

Authors: Noda, Nobuo; Kumeta, Hiroyuki; Nakatogawa, Hitoshi; Satoo, Kenji; Adachi, Wakana; Ishii, Junko; Fujioka, Yuko; Ohsumi, Yoshinori; Inagaki, Fuyuhiko

Citation: Noda, Nobuo; Kumeta, Hiroyuki; Nakatogawa, Hitoshi; Satoo, Kenji; Adachi, Wakana; Ishii, Junko; Fujioka, Yuko; Ohsumi, Yoshinori; Inagaki, Fuyuhiko. "Structural basis of target recognition by Atg8/LC3 during selective autophagy."  Genes Cells 13, 1211-1218 (2008).

Assembly members:
LC3, polymer, 121 residues, 16114.414 Da.
p62_peptide, polymer, 17 residues, Formula weight is not available

Natural source:   Common Name: Rat   Taxonomy ID: 10116   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Rattus norvegicus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
LC3: SMPSEKTFKQRRSFEQRVED VRLIREQHPTKIPVIIERYK GEKQLPVLDKTKFLVPDHVN MSELIKIIRRRLQLNANQAF FLLVNGHSMVSVSTPISEVY ESERDEDGFLYMVYASQETF G
p62_peptide: MSGGDDDWTHLSSKEVD

Data sets:
Data typeCount
13C chemical shifts621
15N chemical shifts146
1H chemical shifts1009

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1LC31
2p62_peptide2

Entities:

Entity 1, LC3 121 residues - 16114.414 Da.

1   SERMETPROSERGLULYSTHRPHELYSGLN
2   ARGARGSERPHEGLUGLNARGVALGLUASP
3   VALARGLEUILEARGGLUGLNHISPROTHR
4   LYSILEPROVALILEILEGLUARGTYRLYS
5   GLYGLULYSGLNLEUPROVALLEUASPLYS
6   THRLYSPHELEUVALPROASPHISVALASN
7   METSERGLULEUILELYSILEILEARGARG
8   ARGLEUGLNLEUASNALAASNGLNALAPHE
9   PHELEULEUVALASNGLYHISSERMETVAL
10   SERVALSERTHRPROILESERGLUVALTYR
11   GLUSERGLUARGASPGLUASPGLYPHELEU
12   TYRMETVALTYRALASERGLNGLUTHRPHE
13   GLY

Entity 2, p62_peptide 17 residues - Formula weight is not available

1   METSERGLYGLYASPASPASPTRPTHRHIS
2   LEUSERSERLYSGLUVALASP

Samples:

LC3_p62: LC3, [U-99% 13C; U-99% 15N], 0.8 mM; p62 peptide 1.2 mM; sodium phosphate 25 mM; sodium chloride 100 mM; H2O 90%; D2O, [U-100% 2H], 10%

p62_LC3: p62 peptide, [U-99% 13C; U-99% 15N], 0.8 mM; LC3 1.2 mM; sodium phosphate 25 mM; sodium chloride 100 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 125 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCLC3_p62isotropicsample_conditions_1
2D 1H-13C HSQCLC3_p62isotropicsample_conditions_1
3D HCCH-TOCSYLC3_p62isotropicsample_conditions_1
3D 1H-13C NOESYLC3_p62isotropicsample_conditions_1
3D 1H-15N NOESYLC3_p62isotropicsample_conditions_1
3D HNCALC3_p62isotropicsample_conditions_1
3D HN(CA)HALC3_p62isotropicsample_conditions_1
3D HBHA(CO)NHLC3_p62isotropicsample_conditions_1
3D C(CO)NHLC3_p62isotropicsample_conditions_1
3D HNCOLC3_p62isotropicsample_conditions_1
3D CCH-TOCSYLC3_p62isotropicsample_conditions_1
2D HbCbCgCdHdLC3_p62isotropicsample_conditions_1
2D HbCbHcCdCeHeLC3_p62isotropicsample_conditions_1
2D 1H-15N HSQCp62_LC3isotropicsample_conditions_1
2D 1H-13C HSQCp62_LC3isotropicsample_conditions_1
3D HNCOp62_LC3isotropicsample_conditions_1
3D HNCAp62_LC3isotropicsample_conditions_1
3D CBCA(CO)NHp62_LC3isotropicsample_conditions_1
3D HBHA(CO)NHp62_LC3isotropicsample_conditions_1
3D HCCH-TOCSYp62_LC3isotropicsample_conditions_1
3D 1H-15N NOESYp62_LC3isotropicsample_conditions_1
3D 1H-13C NOESYp62_LC3isotropicsample_conditions_1

Software:

VNMR v6.1C, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS, Cornilescu, Delaglio and Bax - data analysis

SPARKY v3.110, Goddard - chemical shift assignment, peak picking, refinement

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

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

BMRB 18518
PDB
DBJ BAB15169 BAB22364 BAB22569 BAB22641 BAB22855 BAC26183 BAG35358 BAG53577 BAG65614 BAI46491
EMBL CAD38970 CAL38438 CAA69642 CAH90955
GB AAA20645 AAG09686 AAG23182 AAH18634 AAH41874 AAA93299 AAB02908 AAB17127 AAC50535 AAC52070
REF NP_001001169 NP_001078950 NP_001177219 NP_001180554 NP_001233505 NP_001125548 NP_001135770 NP_001135771 NP_001156515 NP_001253287
SP A6NCE7 O41515 Q62625 Q9CQV6 Q9GZQ8 O08623 Q13501 Q5RBA5 Q64337
TPG DAA20021 DAA28341

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts