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Biological Magnetic Resonance Data Bank


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BMRB Entry 17412

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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/BMR17412
MolProbity Validation Chart

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Title: GABARAPL-1 NBR1-LIR complex structure   PubMed: 21620860

Deposition date: 2011-01-17 Original release date: 2011-06-02

Authors: Rogov, Vladimir; Rozenknop, Alexis; Rogova, Natalia; Loehr, Frank; Guentert, Peter; Dikic, Ivan; Doetsch, Volker

Citation: Rozenknop, Alexis; Rogov, Vladimir; Rogova, Natalia Yu; Lohr, Frank; Guntert, Peter; Dikic, Ivan; Dotsch, Volker. "Characterization of the Interaction of GABARAPL-1 with the LIR Motif of NBR1."  J. Mol. Biol. 410, 477-487 (2011).

Assembly members:
GABARAPL-1, polymer, 119 residues, 14268.327 Da.
NBR1-LIR, polymer, 18 residues, 1840.027 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX4T1

Entity Sequences (FASTA):
GABARAPL-1: GSPEFKFQYKEDHPFEYRKK EGEKIRKKYPDRVPVIVEKA PKARVPDLDKRKYLVPSDLT VGQFYFLIRKRIHLRPEDAL FFFVNNTIPPTSATMGQLYE DNHEEDYFLYVAYSDESVY
NBR1-LIR: GAMGSASSEDYIIILPES

Data sets:
Data typeCount
13C chemical shifts506
15N chemical shifts110
1H chemical shifts881

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1GABARAPL-11
2NBR1-LIR2

Entities:

Entity 1, GABARAPL-1 119 residues - 14268.327 Da.

Residues 1-5 represent a non-native cloning artefact

1   GLYSERPROGLUPHELYSPHEGLNTYRLYS
2   GLUASPHISPROPHEGLUTYRARGLYSLYS
3   GLUGLYGLULYSILEARGLYSLYSTYRPRO
4   ASPARGVALPROVALILEVALGLULYSALA
5   PROLYSALAARGVALPROASPLEUASPLYS
6   ARGLYSTYRLEUVALPROSERASPLEUTHR
7   VALGLYGLNPHETYRPHELEUILEARGLYS
8   ARGILEHISLEUARGPROGLUASPALALEU
9   PHEPHEPHEVALASNASNTHRILEPROPRO
10   THRSERALATHRMETGLYGLNLEUTYRGLU
11   ASPASNHISGLUGLUASPTYRPHELEUTYR
12   VALALATYRSERASPGLUSERVALTYR

Entity 2, NBR1-LIR 18 residues - 1840.027 Da.

Residues 1-4 and 18 represent a non-native cloning artefact

1   GLYALAMETGLYSERALASERSERGLUASP
2   TYRILEILEILELEUPROGLUSER

Samples:

sample_1: GABARAPL-1, [U-98% 15N], 0.6 ± 0.05 mM; NBR1-LIR 0.9 ± 0.05 mM; sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 4.6 mM; protease inhibitor cocktail 1 mM; DSS 0.3 mM; H2O 95%; D2O 5%

sample_2: GABARAPL-1, [U-98% 13C; U-98% 15N], 0.6 ± 0.05 mM; NBR1-LIR 0.9 ± 0.05 mM; sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 4.6 mM; protease inhibitor cocktail 1 mM; DSS 0.3 mM; H2O 95%; D2O 5%

sample_3: GABARAPL-1 0.9 ± 0.05 mM; NBR1-LIR, [U-98% 15N], 0.6 ± 0.05 mM; sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 4.6 mM; protease inhibitor cocktail 1 mM; DSS 0.3 mM; H2O 95%; D2O 5%

sample_4: GABARAPL-1 0.9 ± 0.05 mM; NBR1-LIR, [U-98% 13C; U-98% 15N], 0.6 ± 0.05 mM; sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 4.6 mM; protease inhibitor cocktail 1 mM; DSS 0.3 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
TROSY-H(CCCO)NH-TOCSYsample_2isotropicsample_conditions_1
(H)CC(CO)NH-TOCSYsample_2isotropicsample_conditions_1
3D HNCAsample_4isotropicsample_conditions_1
3D HNCACBsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1
3D H(C)CH-TOCSYsample_4isotropicsample_conditions_1
TROSY-H(CCCO)NH-TOCSYsample_4isotropicsample_conditions_1
(H)CC(CO)NH-TOCSYsample_4isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - structure solution

CSI, Wishart, D. S. & Sykes, B. D. - structure solution

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAA95100 BAB27950 BAB29146 BAB29690 BAB31345
EMBL CAB66611 CAG38511 CAH89636 CAL38063 CAL38067
GB AAH04602 AAH09309 AAH24706 AAH28315 AAH72921
REF NP_001025652 NP_001028788 NP_001037759 NP_001085553 NP_001088067
SP P60518 Q0VGK0 Q5BIZ2 Q5RF21 Q6GQ27
TPG DAA29267
AlphaFold Q5BIZ2 Q6GQ27 Q5RF21 Q0VGK0 P60518

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