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
MolProbity Validation Chart

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Title:
Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif
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:

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).
PubMed: 30990354

Assembly members:

Assembly members:
entity_1, polymer, 116 residues, 13467.532 Da.
entity_2, polymer, 19 residues, 2172.348 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21   Vector: pET39

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MGWMFKEDHSLEHRCVESAK IRAKYPDRVPVIVEKVSGSQ IVDIDKRKYLVPSDITVAQF MWIIRKRIQLPSEKAIFLFV DKTVPQSSLTMGQLYEKEKD EDGFLYVAYSGENTFG
entity_2: GAMEIIHEDNEWGIELVSE

Data sets:
Data typeCount
13C chemical shifts612
15N chemical shifts147
1H chemical shifts1006

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 116 residues - 13467.532 Da.

1   METGLYTRPMETPHELYSGLUASPHISSER
2   LEUGLUHISARGCYSVALGLUSERALALYS
3   ILEARGALALYSTYRPROASPARGVALPRO
4   VALILEVALGLULYSVALSERGLYSERGLN
5   ILEVALASPILEASPLYSARGLYSTYRLEU
6   VALPROSERASPILETHRVALALAGLNPHE
7   METTRPILEILEARGLYSARGILEGLNLEU
8   PROSERGLULYSALAILEPHELEUPHEVAL
9   ASPLYSTHRVALPROGLNSERSERLEUTHR
10   METGLYGLNLEUTYRGLULYSGLULYSASP
11   GLUASPGLYPHELEUTYRVALALATYRSER
12   GLYGLUASNTHRPHEGLY

Entity 2, entity_2 19 residues - 2172.348 Da.

1   GLYALAMETGLUILEILEHISGLUASPASN
2   GLUTRPGLYILEGLULEUVALSERGLU

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D (HCA)CO(CA)NHsample_2isotropicsample_conditions_1
3D (HCA)CO(CA)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D (H)CC(CO)NH-TOCSYsample_2isotropicsample_conditions_1
3D (H)CC(CO)NH-TOCSYsample_1isotropicsample_conditions_1
3D H(CC)(CO)NH-TOCSYsample_2isotropicsample_conditions_1
3D H(CC)(CO)NH-TOCSYsample_1isotropicsample_conditions_1
3D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1sample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1sample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_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 HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks