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- PDB-5lxh: GABARAP-L1 ATG4B LIR Complex -

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Basic information

Entry
Database: PDB / ID: 5lxh
TitleGABARAP-L1 ATG4B LIR Complex
Components
  • Cysteine protease ATG4B
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / LIR / GABARAP / ATG8 / LC3
Function / homology
Function and homology information


protein-phosphatidylethanolamide deconjugating activity / otolith mineralization completed early in development / glycophagy / protein delipidation / microautophagy / aggrephagy / Tat protein binding / protein localization to phagophore assembly site / GABA receptor binding / piecemeal microautophagy of the nucleus ...protein-phosphatidylethanolamide deconjugating activity / otolith mineralization completed early in development / glycophagy / protein delipidation / microautophagy / aggrephagy / Tat protein binding / protein localization to phagophore assembly site / GABA receptor binding / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Macroautophagy / beta-tubulin binding / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / cysteine-type peptidase activity / macroautophagy / cytoplasmic vesicle membrane / protein processing / phospholipid binding / autophagy / protein transport / cytoplasmic vesicle / scaffold protein binding / microtubule / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / proteolysis / cytoplasm / cytosol
Similarity search - Function
Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / ATG4, F-type LIR motif / Peptidase C54 / Peptidase family C54 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) ...Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / ATG4, F-type LIR motif / Peptidase C54 / Peptidase family C54 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein-like 1 / Cysteine protease ATG4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMouilleron, S. / Skytte Rasmussen, M. / Kumar Shrestha, B. / Wirth, M. / Bowitz Larsen, K. / Abudu Princely, Y. / Sjottem, E. / Tooze, S. / Lamark, T. / Johansen, T. / Lee, R.
CitationJournal: Autophagy / Year: 2017
Title: ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8.
Authors: Skytte Rasmussen, M. / Mouilleron, S. / Kumar Shrestha, B. / Wirth, M. / Lee, R. / Bowitz Larsen, K. / Abudu Princely, Y. / O'Reilly, N. / Sjttem, E. / Tooze, S.A. / Lamark, T. / Johansen, T.
History
DepositionSep 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3May 31, 2017Group: Database references
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Gamma-aminobutyric acid receptor-associated protein-like 1
E: Cysteine protease ATG4B
F: Cysteine protease ATG4B
G: Cysteine protease ATG4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,37216
Polymers47,4246
Non-polymers94910
Water3,927218
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
E: Cysteine protease ATG4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9043
Polymers15,8082
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-21 kcal/mol
Surface area6900 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
F: Cysteine protease ATG4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2807
Polymers15,8082
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-47 kcal/mol
Surface area6870 Å2
MethodPISA
3
C: Gamma-aminobutyric acid receptor-associated protein-like 1
G: Cysteine protease ATG4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1886
Polymers15,8082
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-54 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.520, 79.885, 97.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 14598.667 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta, pLysS / References: UniProt: Q9H0R8
#2: Protein/peptide Cysteine protease ATG4B / AUT-like 1 cysteine endopeptidase / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / ...AUT-like 1 cysteine endopeptidase / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / Autophagy-related protein 4 homolog B / hAPG4B


Mass: 1209.257 Da / Num. of mol.: 3 / Fragment: UNP residues 384-393 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9Y4P1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.17 M AMSO4, 40 % PEG 4000, 15 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.58→51 Å / Num. obs: 55946 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rsym value: 0.05 / Net I/σ(I): 10.7
Reflection shellResolution: 1.58→1.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2Q

2r2q


Resolution: 1.58→48.822 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 2721 4.89 %0.224
Rwork0.2053 ---
obs0.2069 55665 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→48.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 53 218 3353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173344
X-RAY DIFFRACTIONf_angle_d1.4284552
X-RAY DIFFRACTIONf_dihedral_angle_d20.6022040
X-RAY DIFFRACTIONf_chiral_restr0.083470
X-RAY DIFFRACTIONf_plane_restr0.009590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60870.45661470.39122720X-RAY DIFFRACTION98
1.6087-1.63970.39511350.39372704X-RAY DIFFRACTION98
1.6397-1.67310.37581550.36732729X-RAY DIFFRACTION99
1.6731-1.70950.36081440.34332720X-RAY DIFFRACTION99
1.7095-1.74930.34931600.32422730X-RAY DIFFRACTION99
1.7493-1.7930.34271400.28012755X-RAY DIFFRACTION99
1.793-1.84150.27241440.25612784X-RAY DIFFRACTION99
1.8415-1.89570.2841110.24562769X-RAY DIFFRACTION100
1.8957-1.95690.30731400.24282744X-RAY DIFFRACTION99
1.9569-2.02690.28851510.22222755X-RAY DIFFRACTION100
2.0269-2.1080.23471520.19922787X-RAY DIFFRACTION100
2.108-2.20390.19641250.18912796X-RAY DIFFRACTION100
2.2039-2.32010.23511550.192778X-RAY DIFFRACTION100
2.3201-2.46550.23371410.19032809X-RAY DIFFRACTION100
2.4655-2.65580.22811580.19592779X-RAY DIFFRACTION100
2.6558-2.92310.20661360.19052827X-RAY DIFFRACTION100
2.9231-3.3460.21381490.18152864X-RAY DIFFRACTION100
3.346-4.21520.18441260.15362885X-RAY DIFFRACTION100
4.2152-48.84490.19651520.18013009X-RAY DIFFRACTION100

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