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- PDB-2l8j: GABARAPL-1 NBR1-LIR complex structure -

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Basic information

Entry
Database: PDB / ID: 2l8j
TitleGABARAPL-1 NBR1-LIR complex structure
Components
  • Gamma-aminobutyric acid receptor-associated protein-like 1
  • NBR1-LIR peptide
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / selective autophagy / LC3 proteins / SIGNALING PROTEIN / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


glycophagy / Tat protein binding / GABA receptor binding / cellular response to nitrogen starvation / regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / Macroautophagy ...glycophagy / Tat protein binding / GABA receptor binding / cellular response to nitrogen starvation / regulation of bone mineralization / phagophore assembly site / M band / peroxisomal membrane / mitogen-activated protein kinase binding / Macroautophagy / regulation of stress-activated MAPK cascade / beta-tubulin binding / autophagosome membrane / autophagosome assembly / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding / phospholipid binding / macroautophagy / cytoplasmic vesicle membrane / mitochondrial intermembrane space / late endosome / microtubule / lysosome / nuclear body / receptor complex / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / zinc ion binding / nucleoplasm / membrane / cytosol
Similarity search - Function
NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / PB1 domain / Zinc finger ZZ-type signature. ...NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / PB1 domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Next to BRCA1 gene 1 protein / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / energy minimization
Model detailslowest energy, model 1
AuthorsRogov, V.V. / Rozenknop, A. / Rogova, N.Y. / Loehr, F. / Guentert, P. / Dikic, I. / Doetsch, V.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Characterization of the Interaction of GABARAPL-1 with the LIR Motif of NBR1.
Authors: Rozenknop, A. / Rogov, V.V. / Rogova, N.Y. / Lohr, F. / Guntert, P. / Dikic, I. / Dotsch, V.
History
DepositionJan 17, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: NBR1-LIR peptide


Theoretical massNumber of molelcules
Total (without water)16,1082
Polymers16,1082
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14268.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / Strain (production host): NEBT7 / References: UniProt: Q9H0R8
#2: Protein/peptide NBR1-LIR peptide


Mass: 1840.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): NEBT7 / References: UniProt: Q14596

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution structure of the complex between a MAP1LC3 protein, GABARAPL-1, and the LIR motif of NBR1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-15N HSQC
1322D 1H-13C HSQC
1442D 1H-13C HSQC aliphatic
1542D 1H-13C HSQC aromatic
1642D 1H-13C HSQC
1723D HNCO
1823D HN(CA)CO
1923D HNCA
11023D HN(CA)CB
11123D 1H-15N NOESY
11223D 1H-13C NOESY
1132TROSY-H(CCCO)NH-TOCSY
1142(H)CC(CO)NH-TOCSY
11543D HNCA
11643D HN(CA)CB
11743D 1H-15N NOESY
11843D 1H-13C NOESY
11943D (H)CCH-TOCSY
1204TROSY-H(CCCO)NH-TOCSY
1214(H)CC(CO)NH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-98% 15N] GABARAPL-1, 0.9 mM NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.6 mM [U-98% 13C; U-98% 15N] GABARAPL-1, 0.9 mM NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.9 mM GABARAPL-1, 0.6 mM [U-98% 15N] NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
40.9 mM GABARAPL-1, 0.6 mM [U-98% 13C; U-98% 15N] NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMGABARAPL-1-1[U-98% 15N]1
0.9 mMNBR1-LIR-21
50 mMsodium phosphate-31
100 mMsodium chloride-41
4.6 mMsodium azide-51
1 mMprotease inhibitor cocktail-61
0.3 mMDSS-71
0.6 mMGABARAPL-1-8[U-98% 13C; U-98% 15N]2
0.9 mMNBR1-LIR-92
50 mMsodium phosphate-102
100 mMsodium chloride-112
4.6 mMsodium azide-122
1 mMprotease inhibitor cocktail-132
0.3 mMDSS-142
0.9 mMGABARAPL-1-153
0.6 mMNBR1-LIR-16[U-98% 15N]3
50 mMsodium phosphate-173
100 mMsodium chloride-183
4.6 mMsodium azide-193
1 mMprotease inhibitor cocktail-203
0.3 mMDSS-213
0.9 mMGABARAPL-1-224
0.6 mMNBR1-LIR-23[U-98% 13C; U-98% 15N]4
50 mMsodium phosphate-244
100 mMsodium chloride-254
4.6 mMsodium azide-264
1 mMprotease inhibitor cocktail-274
0.3 mMDSS-284
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxstructure solution
CSIWishart, D. S. & Sykes, B. D.structure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: energy minimization / Software ordinal: 1
NMR constraintsNOE constraints total: 1448 / NOE intraresidue total count: 207 / NOE long range total count: 510 / NOE medium range total count: 245 / NOE sequential total count: 436 / Hydrogen bond constraints total count: 84
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.09 Å
NMR ensemble rmsDistance rms dev: 0.0081 Å / Distance rms dev error: 0.0004 Å

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