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

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Basic information

Entry
Database: PDB / ID: 5lxi
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


otolith mineralization completed early in development / protein-phosphatidylethanolamide deconjugating activity / protein delipidation / microautophagy / glycophagy / aggrephagy / Tat protein binding / GABA receptor binding / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus ...otolith mineralization completed early in development / protein-phosphatidylethanolamide deconjugating activity / protein delipidation / microautophagy / glycophagy / aggrephagy / Tat protein binding / GABA receptor binding / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phosphatidylethanolamine binding / cellular response to nitrogen starvation / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome assembly / mitophagy / autophagosome maturation / cysteine-type peptidase activity / autophagosome / macroautophagy / cytoplasmic vesicle membrane / protein processing / phospholipid binding / autophagy / protein transport / scaffold protein binding / cytoplasmic vesicle / endopeptidase activity / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / mitochondrion / proteolysis / cytosol / cytoplasm
Similarity search - Function
Peptidase C54 / Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / Peptidase family C54 / ATG4, F-type LIR motif / 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 / Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / Peptidase family C54 / ATG4, F-type LIR motif / 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
DI(HYDROXYETHYL)ETHER / PEROXIDE ION / TRIETHYLENE GLYCOL / 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: 1.44 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 1.1Mar 22, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Gamma-aminobutyric acid receptor-associated protein-like 1
C: Cysteine protease ATG4B
E: Cysteine protease ATG4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,38113
Polymers31,7764
Non-polymers6059
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.888, 72.377, 30.620
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules DBCE

#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.: 2
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: 1289.236 Da / Num. of mol.: 2 / 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

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Non-polymers , 6 types, 109 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MgCl2, 24.6 % PEG 400, 29.5 % PEG 8000, 0.1M TRIS 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.44→35 Å / Num. obs: 46217 / % possible obs: 96 % / Redundancy: 3.1 % / CC1/2: 0.998 / Rsym value: 0.038 / Net I/σ(I): 10.1
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.74 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r2q

2r2q


Resolution: 1.44→31.207 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2265 4.9 %
Rwork0.1969 --
obs0.1987 46205 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→31.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 38 100 2216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142252
X-RAY DIFFRACTIONf_angle_d1.1593056
X-RAY DIFFRACTIONf_dihedral_angle_d22.708875
X-RAY DIFFRACTIONf_chiral_restr0.101313
X-RAY DIFFRACTIONf_plane_restr0.008399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.47130.41771400.36372648X-RAY DIFFRACTION92
1.4713-1.50550.40551180.32852668X-RAY DIFFRACTION92
1.5055-1.54320.33811380.31022676X-RAY DIFFRACTION92
1.5432-1.58490.35631160.30142667X-RAY DIFFRACTION93
1.5849-1.63160.32421380.27532683X-RAY DIFFRACTION94
1.6316-1.68420.33451240.24872754X-RAY DIFFRACTION94
1.6842-1.74440.28061240.23422706X-RAY DIFFRACTION94
1.7444-1.81420.26441210.21922777X-RAY DIFFRACTION95
1.8142-1.89680.27091630.20012735X-RAY DIFFRACTION95
1.8968-1.99680.24851650.18952731X-RAY DIFFRACTION96
1.9968-2.12190.22951380.17722806X-RAY DIFFRACTION96
2.1219-2.28560.25961540.18322776X-RAY DIFFRACTION97
2.2856-2.51560.24531690.18962798X-RAY DIFFRACTION97
2.5156-2.87940.22921270.18992821X-RAY DIFFRACTION97
2.8794-3.62680.19421520.17552846X-RAY DIFFRACTION98
3.6268-31.21470.17171780.16442848X-RAY DIFFRACTION97

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