BMRB Entry 34307
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR34307
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Title: Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif PubMed: 30990354
Deposition date: 2018-08-02 Original release date: 2019-04-24
Authors: Huber, J.; Loehr, F.; Gruber, J.; Akutsu, M.; Guentert, P.; Doetsch, V.; Rogov, V.
Citation: Huber, Jessica; Obata, Miki; Gruber, Jens; Akutsu, Masato; Lohr, Frank; Rogova, Natalia; Guntert, Peter; Dikic, Ivan; Kirkin, Vladimir; Komatsu, Masaaki; Dotsch, Volker; Rogov, Vladimir. "An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5" Autophagy ., 1-15 (2019).
Assembly members:
entity_1, polymer, 116 residues, 13467.532 Da.
entity_2, polymer, 19 residues, 2172.348 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21
Entity Sequences (FASTA):
entity_1: MGWMFKEDHSLEHRCVESAK
IRAKYPDRVPVIVEKVSGSQ
IVDIDKRKYLVPSDITVAQF
MWIIRKRIQLPSEKAIFLFV
DKTVPQSSLTMGQLYEKEKD
EDGFLYVAYSGENTFG
entity_2: GAMEIIHEDNEWGIELVSE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 612 |
| 15N chemical shifts | 147 |
| 1H chemical shifts | 1006 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
Entities:
Entity 1, entity_1 116 residues - 13467.532 Da.
| 1 | MET | GLY | TRP | MET | PHE | LYS | GLU | ASP | HIS | SER | ||||
| 2 | LEU | GLU | HIS | ARG | CYS | VAL | GLU | SER | ALA | LYS | ||||
| 3 | ILE | ARG | ALA | LYS | TYR | PRO | ASP | ARG | VAL | PRO | ||||
| 4 | VAL | ILE | VAL | GLU | LYS | VAL | SER | GLY | SER | GLN | ||||
| 5 | ILE | VAL | ASP | ILE | ASP | LYS | ARG | LYS | TYR | LEU | ||||
| 6 | VAL | PRO | SER | ASP | ILE | THR | VAL | ALA | GLN | PHE | ||||
| 7 | MET | TRP | ILE | ILE | ARG | LYS | ARG | ILE | GLN | LEU | ||||
| 8 | PRO | SER | GLU | LYS | ALA | ILE | PHE | LEU | PHE | VAL | ||||
| 9 | ASP | LYS | THR | VAL | PRO | GLN | SER | SER | LEU | THR | ||||
| 10 | MET | GLY | GLN | LEU | TYR | GLU | LYS | GLU | LYS | ASP | ||||
| 11 | GLU | ASP | GLY | PHE | LEU | TYR | VAL | ALA | TYR | SER | ||||
| 12 | GLY | GLU | ASN | THR | PHE | GLY |
Entity 2, entity_2 19 residues - 2172.348 Da.
| 1 | GLY | ALA | MET | GLU | ILE | ILE | HIS | GLU | ASP | ASN | ||||
| 2 | GLU | TRP | GLY | ILE | GLU | LEU | VAL | SER | GLU |
Samples:
sample_1: GABARAPL2, [U-99% 13C; U-99% 15N], 0.6 ± 0.05 mM; Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif 1.0 ± 0.05 mM; sodium phosphate 50 ± 1 mM; sodium chloride 100 ± 1 mM; sodium azide 4.6 ± 0.1 mM
sample_2: GABARAPL2 1.0 ± 0.05 mM; Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, [U-99% 13C; U-99% 15N], 0.6 ± 0.05 mM; sodium phosphate 50 ± 1 mM; sodium chloride 100 ± 1 mM; sodium azide 4.6 ± 0.1 mM
sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D (HCA)CO(CA)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D (HCA)CO(CA)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D (H)CC(CO)NH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D (H)CC(CO)NH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CC)(CO)NH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D H(CC)(CO)NH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1 | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1 | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
TOPSPIN v3.1, Bruker Biospin - collection
SPARKY v1.114, Goddard - chemical shift assignment
CYANA v3.97, Guntert, Mumenthaler and Wuthrich - peak picking, structure calculation
OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement
NMR spectrometers:
- Bruker Bruker Avance 950 MHz 950 MHz
- Bruker Bruker Avance 900 MHz 900 MHz
- Bruker Bruker Avance 800 MHz 800 MHz
- Bruker Bruker Avance 700 MHz 700 MHz
- Bruker Bruker Avance 600 MHz 600 MHz
- Bruker Bruker Avance 500 MHz 500 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts