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
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
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).
PubMed: 19021777
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 Vector: pGEX6p
Entity Sequences (FASTA):
LC3: SMPSEKTFKQRRSFEQRVED
VRLIREQHPTKIPVIIERYK
GEKQLPVLDKTKFLVPDHVN
MSELIKIIRRRLQLNANQAF
FLLVNGHSMVSVSTPISEVY
ESERDEDGFLYMVYASQETF
G
p62_peptide: MSGGDDDWTHLSSKEVD
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 621 |
| 15N chemical shifts | 146 |
| 1H chemical shifts | 1009 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | LC3 | 1 |
| 2 | p62_peptide | 2 |
Entities:
Entity 1, LC3 121 residues - 16114.414 Da.
| 1 | SER | MET | PRO | SER | GLU | LYS | THR | PHE | LYS | GLN | ||||
| 2 | ARG | ARG | SER | PHE | GLU | GLN | ARG | VAL | GLU | ASP | ||||
| 3 | VAL | ARG | LEU | ILE | ARG | GLU | GLN | HIS | PRO | THR | ||||
| 4 | LYS | ILE | PRO | VAL | ILE | ILE | GLU | ARG | TYR | LYS | ||||
| 5 | GLY | GLU | LYS | GLN | LEU | PRO | VAL | LEU | ASP | LYS | ||||
| 6 | THR | LYS | PHE | LEU | VAL | PRO | ASP | HIS | VAL | ASN | ||||
| 7 | MET | SER | GLU | LEU | ILE | LYS | ILE | ILE | ARG | ARG | ||||
| 8 | ARG | LEU | GLN | LEU | ASN | ALA | ASN | GLN | ALA | PHE | ||||
| 9 | PHE | LEU | LEU | VAL | ASN | GLY | HIS | SER | MET | VAL | ||||
| 10 | SER | VAL | SER | THR | PRO | ILE | SER | GLU | VAL | TYR | ||||
| 11 | GLU | SER | GLU | ARG | ASP | GLU | ASP | GLY | PHE | LEU | ||||
| 12 | TYR | MET | VAL | TYR | ALA | SER | GLN | GLU | THR | PHE | ||||
| 13 | GLY |
Entity 2, p62_peptide 17 residues - Formula weight is not available
| 1 | MET | SER | GLY | GLY | ASP | ASP | ASP | TRP | THR | HIS | ||||
| 2 | LEU | SER | SER | LYS | GLU | VAL | ASP |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | LC3_p62 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | LC3_p62 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | LC3_p62 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | LC3_p62 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | LC3_p62 | isotropic | sample_conditions_1 |
| 3D HNCA | LC3_p62 | isotropic | sample_conditions_1 |
| 3D HN(CA)HA | LC3_p62 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | LC3_p62 | isotropic | sample_conditions_1 |
| 3D C(CO)NH | LC3_p62 | isotropic | sample_conditions_1 |
| 3D HNCO | LC3_p62 | isotropic | sample_conditions_1 |
| 3D CCH-TOCSY | LC3_p62 | isotropic | sample_conditions_1 |
| 2D HbCbCgCdHd | LC3_p62 | isotropic | sample_conditions_1 |
| 2D HbCbHcCdCeHe | LC3_p62 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | p62_LC3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | p62_LC3 | isotropic | sample_conditions_1 |
| 3D HNCO | p62_LC3 | isotropic | sample_conditions_1 |
| 3D HNCA | p62_LC3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | p62_LC3 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | p62_LC3 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | p62_LC3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | p62_LC3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | p62_LC3 | isotropic | sample_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 |
| AlphaFold | A6NCE7 O41515 Q62625 Q9CQV6 Q9GZQ8 O08623 Q13501 Q5RBA5 Q64337 |
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated peaks
SPARKY: Backbone
or all simulated peaks