BMRB Entry 18518
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18518
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Title: LC3B OPTN-LIR Ptot complex structure PubMed: 23805866
Deposition date: 2012-06-13 Original release date: 2013-07-15
Authors: Rogov, Vladimir; Rozenknop, Alexis; Loehr, Frank; Guentert, Peter; Doetsch, Volker
Citation: Rogov, Vladimir; Suzuki, Hironori; Fiskin, Evgenij; Wild, Philipp; Kniss, Andreas; Rozenknop, Alexis; Kato, Ryuichi; Kawasaki, Masato; McEwan, David; Lohr, Frank; Guntert, Peter; Dikic, Ivan; Wakatsuki, Soichi; Dotsch, Volker. "Structural basis for phosphorylation-triggered autophagic clearance of Salmonella." Biochem. J. 454, 459-466 (2013).
Assembly members:
entity_1, polymer, 119 residues, 13965.232 Da.
entity_2, polymer, 17 residues, 2245.827 Da.
Natural source: Common Name: Humans Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: GAMGKTFKQRRTFEQRVEDV
RLIREQHPTKIPVIIERYKG
EKQLPVLDKTKFLVPDHVNM
SELIKIIRRRLQLNANQAFF
LLVNGHSMVSVSTPISEVYE
SEKDEDGFLYMVYASQETF
entity_2: NXXGXXEDXFVEIRMAE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 548 |
| 15N chemical shifts | 141 |
| 1H chemical shifts | 1028 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 119 residues - 13965.232 Da.
Residues 1-4 are expression tag. Residues 5-119 correspond to residues 5-119 of human Microtubule-associated proteins 1A/1B light chain 3B (UniProtKB entry Q9GZQ8)
| 1 | GLY | ALA | MET | GLY | LYS | THR | PHE | LYS | GLN | ARG | ||||
| 2 | ARG | THR | PHE | GLU | GLN | ARG | VAL | GLU | ASP | VAL | ||||
| 3 | ARG | LEU | ILE | ARG | GLU | GLN | HIS | PRO | THR | LYS | ||||
| 4 | ILE | PRO | VAL | ILE | ILE | GLU | ARG | TYR | LYS | GLY | ||||
| 5 | GLU | LYS | GLN | LEU | PRO | VAL | LEU | ASP | LYS | THR | ||||
| 6 | LYS | PHE | LEU | VAL | PRO | ASP | HIS | VAL | ASN | MET | ||||
| 7 | SER | GLU | LEU | ILE | LYS | ILE | ILE | ARG | ARG | ARG | ||||
| 8 | LEU | GLN | LEU | ASN | ALA | ASN | GLN | ALA | PHE | PHE | ||||
| 9 | LEU | LEU | VAL | ASN | GLY | HIS | SER | MET | VAL | SER | ||||
| 10 | VAL | SER | THR | PRO | ILE | SER | GLU | VAL | TYR | GLU | ||||
| 11 | SER | GLU | LYS | ASP | GLU | ASP | GLY | PHE | LEU | TYR | ||||
| 12 | MET | VAL | TYR | ALA | SER | GLN | GLU | THR | PHE |
Entity 2, entity_2 17 residues - 2245.827 Da.
Residues 169-185 correspond to residues 169-185 of human Optineurin sequence (UniProtKB entry Q96CV9). All serines in the peptide are phosphoserines (SEP).
| 1 | ASN | SEP | SEP | GLY | SEP | SEP | GLU | ASP | SEP | PHE | ||||
| 2 | VAL | GLU | ILE | ARG | MET | ALA | GLU |
Samples:
sample_1: entity_1, [U-98% 13C; U-98% 15N], 0.6 ± 0.05 mM; entity_2 4.9 ± 0.5 mM; sodium phosphate 70 mM; sodium chloride 30 mM; DSS 0.3 mM; Protease inhibitors cocktail 5 mM; H2O 95%; D2O 5%
sample_2: entity_1, [U-98% 13C; U-98% 15N], 2.5 ± 0.05 mM; entity_2 0.4 ± 0.04 mM; sodium phosphate 70 mM; sodium chloride 30 mM; DSS 0.3 mM; Protease inhibitors cocktail 5 mM; H2O 95%; D2O 5%
sample_conditions_1: ionic strength: 0.05 M; pH: 6.8; pressure: 1 atm; temperature: 288 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 3D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1 | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY F1,F2 13C/15N filtered | sample_2 | isotropic | sample_conditions_1 |
| 3D NOESY-[15N,1H]-FHSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
TOPSPIN v2, Bruker Biospin - chemical shift calculation, collection, processing
SPARKY v3.114, Goddard - chemical shift assignment, data analysis, peak picking
CYANA v2, Guntert, Mumenthaler and Wuthrich - structure solution
OPALp, Koradi, Billeter and Guntert - refinement
NMR spectrometers:
- Bruker Avance 900 MHz
- Bruker Avance 800 MHz
- Bruker Avance 700 MHz
- Bruker Avance 600 MHz
- Bruker Avance 500 MHz
Related Database Links:
| UNP | Q9GZQ8 Q96CV9 |
| BMRB | 15877 |
| PDB | |
| DBJ | BAB15169 BAB22364 BAB22569 BAB22641 BAB22855 |
| EMBL | CAD38970 CAG31435 CAL38438 |
| GB | AAA20645 AAB72082 AAG09686 AAG23182 AAH18634 |
| REF | NP_001001169 NP_001026632 NP_001078950 NP_001177219 NP_001180554 |
| SP | A6NCE7 O41515 Q62625 Q9CQV6 Q9GZQ8 |
| TPG | DAA20021 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts