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2l8j

GABARAPL-1 NBR1-LIR complex structure

Method: SOLUTION NMR Dmax: 54.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Gamma-aminobutyric acid receptor-associated protein-like 1

Homo sapiens

UniProt Q9H0R8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–115 Not recorded NBR1-LIR peptide × 1 （Q14596） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.6 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% D2O | 95% H2O/5% D2O NMR sample composition：0.6 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% D2O | 95% H2O/5% D2O NMR sample composition：0.9 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% D2O | 95% H2O/5% D2O NMR sample composition：0.9 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% D2O | 95% H2O/5% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2L8J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2R2Q Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a Deposited 2007-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–111（109 aa）
Not recorded UNX UNKNOWN LIGAND × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.65 Å R-free 0.234
2R2Q Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a Deposited 2007-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3–111（109 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K
Resolution 1.65 Å R-free 0.234
5DPT Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117 Deposited 2015-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–117（116 aa） Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；278 K；20% w/v Polyethylene glycol 3,350, 0.2 M NaCl, 8% MPD pH 7.2
Resolution 2.90 Å R-free 0.260
5DPT Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117 Deposited 2015-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–117（116 aa） Fragment：UNP Q9Y4G2 627-638, UNP Q9H0R8 2-117
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；278 K；20% w/v Polyethylene glycol 3,350, 0.2 M NaCl, 8% MPD pH 7.2
Resolution 2.90 Å R-free 0.260
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Resolution 1.58 Å R-free 0.237
5LXH GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–117（117 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol
Resolution 1.58 Å R-free 0.237
5LXI GABARAP-L1 ATG4B LIR Complex Deposited 2016-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–117（117 aa）
Chain D 1–117（117 aa）
Not recorded MG MAGNESIUM ION × 3 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 1 PER PEROXIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5
Resolution 1.44 Å R-free 0.230
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000
Resolution 1.14 Å R-free 0.166
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000
Resolution 1.14 Å R-free 0.166
6HOL Structure of ATG14 LIR motif bound to GABARAPL1 Deposited 2018-09-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；1M LiCl, 0.1M HEPES pH7, 20% PEG 6000
Resolution 1.40 Å R-free 0.203
6HOL Structure of ATG14 LIR motif bound to GABARAPL1 Deposited 2018-09-17 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；289 K；1M LiCl, 0.1M HEPES pH7, 20% PEG 6000
Resolution 1.40 Å R-free 0.203
6YOO Structure of SAMM50 LIR bound to GABARAPL1 Deposited 2020-04-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24% w/v PEG 6000, 10 mM ZnCl2 and 0.1 M Tris pH 7.5
Resolution 1.06 Å R-free 0.147
7AA7 Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded SAT sulfoacetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES pH 6.5, 3.5M AMSO4, 1% MPD
Resolution 1.45 Å R-free 0.189
7AA7 Structure of SCOC pS12/pS18 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded SAT sulfoacetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES pH 6.5, 3.5M AMSO4, 1% MPD
Resolution 1.45 Å R-free 0.189
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8
Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8
Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8
Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8
Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8
Resolution 1.72 Å R-free 0.261
7AA9 Structure of SCOC pT13/pT15 LIR motif bound to GABARAPL1 Deposited 2020-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 1500 0.1M TRIS 8
Resolution 1.72 Å R-free 0.261
7JHX Crystal structure of hEPG5 LIR/GABARAPL1 complex Deposited 2020-07-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M ammonium sulfate, 0.1 MES buffer pH 5.5, 29% (w/v) PEG 4000
Resolution 1.91 Å R-free 0.245
7JHX Crystal structure of hEPG5 LIR/GABARAPL1 complex Deposited 2020-07-21 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M ammonium sulfate, 0.1 MES buffer pH 5.5, 29% (w/v) PEG 4000
Resolution 1.91 Å R-free 0.245
8X8A Crystal structure of STBD1 LIR motif in complex with GABARAPL1 Deposited 2023-11-27 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；25% w/v Pentaerythritol Propoxylate (5/4 PO/OH), 0.1 M Sodium acetate pH 4.6, 0.05 M Magnesium chloride
Resolution 1.53 Å R-free 0.187
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol
Resolution 2.52 Å R-free 0.259
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–117（117 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol
Resolution 2.52 Å R-free 0.259
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–117（117 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol
Resolution 2.52 Å R-free 0.259
9HGC Crystal structure of human GABARAPL1 in complex with cyclic peptide GAB_D8 Deposited 2024-11-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–117（117 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.17 M ammonium sulfate, 25.5% PEG 4000, 15% glycerol
Resolution 2.52 Å R-free 0.259
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–117（117 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000
Resolution 1.76 Å R-free 0.215
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–117（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000
Resolution 1.76 Å R-free 0.215

13 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GBRL1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–119； UniProt 2–115

NBR1-LIR peptide

Homo sapiens

UniProt Q14596

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 726–738 Not recorded Gamma-aminobutyric acid receptor-associated protein-like 1 × 1 （Q9H0R8） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.6 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% D2O | 95% H2O/5% D2O NMR sample composition：0.6 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% D2O | 95% H2O/5% D2O NMR sample composition：0.9 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% D2O | 95% H2O/5% D2O NMR sample composition：0.9 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% D2O | 95% H2O/5% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2L8J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WJ6 Solution structure of RSGI RUH-024, a PB1 domain in human cDNA, KIAA0049 Deposited 2004-05-29 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–88（88 aa） Fragment：PB1 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient
NMR sample composition 1.15mM PB1 domain U-15N,13C; 20mM Tris-HCl buffer (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2BKF Structure of the PB1 domain of NBR1 Deposited 2005-02-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–85（85 aa） Fragment：RESIDUES 1-85 (PB1 INTERACTION DOMAIN)
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.1；1.6 M AMMONIUM SULFATE,0.1 M SODIUM ACETATE PH 4.1
Resolution 1.56 Å R-free 0.226
2CP8 Solution structure of the RSGI RUH-046, a UBA domain from human Next to BRCA1 gene 1 protein (KIAA0049 protein) R923H variant Deposited 2005-05-19 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 916–956（41 aa） Fragment：UBA
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient
NMR sample composition 2.62mM RSGI RUH-046 U-13C, 15N; 20mM Tris-HCl U-2H, 100mM NaCl, 1mM DTT U-2H, 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2G4S Anomalous substructure of NBR1PB1 Deposited 2006-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–85（85 aa） Fragment：PB1 domain
Not recorded CL CHLORIDE ION × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.15 Å R-free 0.323
2MGW Solution Structure of the UBA Domain of Human NBR1 Deposited 2013-11-09 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 913–959（47 aa） Fragment：UNP residues 913-959
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Pressure ambient
NMR sample composition 20 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium phosphate-8, 5 mM potassium chloride-9, 1 mM EDTA-10, 1 mM benzamidine-11, 1 mM DTT-12, 0.02 % sodium azide-13, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-14, 12.5 mg/mL Pf1 phage-15, 150 mM sodium chloride-16, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MJ5 Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin Deposited 2013-12-25 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 913–959（47 aa） Fragment：UNP residues 916-959
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.6；298 K；Pressure ambient
NMR sample composition 20 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95 % H2O-8, 5 % D2O-9, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium phosphate-10, 5 mM potassium chloride-11, 1 mM EDTA-12, 1 mM benzamidine-13, 1 mM DTT-14, 0.02 % sodium azide-15, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-16, 12.5 mg/mL Pf1 phage-17, 150 mM sodium chloride-18, 95 % H2O-19, 5 % D2O-20, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-21, 2 mM Ubiquitin-22, 12.5 mg/mL Pf1 phage-23, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium phosphate-24, 5 mM potassium chloride-25, 1 mM EDTA-26, 1 mM benzamidine-27, 1 mM DTT-28, 0.02 % sodium azide-29, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-30, 12.5 mg/mL Pf1 phage-31, 150 mM sodium chloride-32, 95 % H2O-33, 5 % D2O-34, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-35, 2 mM Ubiquitin-36, 12.5 mg/mL Pf1 phage-37, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2 mM NBR1_UBA-38, 0.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-39, 12.5 mg/mL Pf1 phage-40, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-100% 15N] NBR1_UBA-41, 4.5 mM Ubiquitin-42, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 365–485（121 aa） Fragment：UNP residues 365-485
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 365–485（121 aa） Fragment：UNP residues 365-485
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 365–485（121 aa） Fragment：UNP residues 365-485
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 365–485（121 aa） Fragment：UNP residues 365-485
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric
Chain A 365–485（121 aa） Fragment：UNP residues 365-485
Chain B 365–485（121 aa） Fragment：UNP residues 365-485
Chain C 365–485（121 aa） Fragment：UNP residues 365-485
Chain D 365–485（121 aa） Fragment：UNP residues 365-485
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 28 EDO 1,2-ETHANEDIOL × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.52 Å R-free 0.188

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NBR1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–17； UniProt 726–738

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2l8j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2l8j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2l8j
Deposition date deposition_date2011-01-17
Structure title titleGABARAPL-1 NBR1-LIR complex structure
Keywords keywordsselective autophagy, LC3 proteins, SIGNALING PROTEIN, SIGNALING PROTEIN-PROTEIN BINDING complex; SIGNALING PROTEIN/PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.96 Å
Radius of gyration Rg (electron density) rg_electron15.46 Å
Forward intensity I(0) i01307490000.00
Molecular weight molecular_weight320960.0 kDa
Excluded volume excluded_volume406270 ų
Envelope volume envelope_volume42040 ų
Hydration-shell volume shell_volume19409 ų
Envelope diameter envelope_diameter62.7 Å
Shell Rg shell_rg24.60 Å
Envelope Rg envelope_rg18.19 Å
Shape Rg shape_rg15.42 Å
Total Rg total_rg15.76 Å
Total atoms total_atoms44960
Residues n_residues2740
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax54.7 Å
Rg (real space) rg_real15.90 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.3070e+09
I(0) uncertainty (real space) i0_real_error1.6610e+07
Rg (reciprocal space) rg_reciprocal15.91 Å
I(0) (reciprocal space) i0_reciprocal1307000000.0000
Solution quality estimate total_estimate0.7754
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.8 Å
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.184
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha694800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.698; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2l8ja1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.3 — GABARAP-like
Domain ID domain_idd2l8ja2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2l8jA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)