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- PDB-2z0e: The crystal structure of human Atg4B- LC3(1-124) complex -

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Basic information

Entry
Database: PDB / ID: 2z0e
TitleThe crystal structure of human Atg4B- LC3(1-124) complex
Components
  • Cysteine protease ATG4B
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsHYDROLASE/STRUCTURAL PROTEIN / papain-like fold / ubiquitin fold / HYDROLASE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


otolith mineralization completed early in development / Receptor Mediated Mitophagy / protein-phosphatidylethanolamide deconjugating activity / TBC/RABGAPs / Pexophagy / PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / positive regulation of mucus secretion / Macroautophagy / protein delipidation ...otolith mineralization completed early in development / Receptor Mediated Mitophagy / protein-phosphatidylethanolamide deconjugating activity / TBC/RABGAPs / Pexophagy / PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / positive regulation of mucus secretion / Macroautophagy / protein delipidation / microautophagy / aggrephagy / ceramide binding / mucus secretion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phosphatidylethanolamine binding / cellular response to nitrogen starvation / microtubule associated complex / Macroautophagy / autolysosome / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / cysteine-type peptidase activity / tubulin binding / autophagosome / cellular response to starvation / macroautophagy / establishment of localization in cell / mitochondrial membrane / protein processing / autophagy / protein transport / presynapse / cytoplasmic vesicle / scaffold protein binding / endopeptidase activity / microtubule binding / microtubule / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein domain specific binding / axon / cysteine-type endopeptidase activity / neuronal cell body / dendrite / ubiquitin protein ligase binding / endoplasmic reticulum / mitochondrion / proteolysis / membrane / cytoplasm / cytosol
Similarity search - Function
Peptidase C54 / Peptidase C54, catalytic domain / Cysteine protease ATG4, F-type LIR motif / Peptidase C54 catalytic domain / 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 C54 catalytic domain / 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
Microtubule-associated protein 1 light chain 3 beta / Cysteine protease ATG4B
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSatoo, K. / Noda, N.N. / Inagaki, F.
CitationJournal: Embo J. / Year: 2009
Title: The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.
Authors: Satoo, K. / Noda, N.N. / Kumeta, H. / Fujioka, Y. / Mizushima, N. / Ohsumi, Y. / Inagaki, F.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine protease ATG4B
B: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)55,0442
Polymers55,0442
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-9 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.850, 90.883, 102.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hetero-dimer of molecules A and B.

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Components

#1: Protein Cysteine protease ATG4B / HsAtg4B / Autophagy-related protein 4 homolog B / hAPG4B / Autophagin-1 / Autophagy-related ...HsAtg4B / Autophagy-related protein 4 homolog B / hAPG4B / Autophagin-1 / Autophagy-related cysteine endopeptidase 1 / AUT-like 1 cysteine endopeptidase


Mass: 40111.621 Da / Num. of mol.: 1 / Fragment: residues (-2)-354 / Mutation: H280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9Y4P1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Microtubule-associated proteins 1A/1B light chain 3B / LC3 / Microtubule-associated protein 1 light chain 3 beta / MAP1A/MAP1B LC3 B / MAP1A/1B light ...LC3 / Microtubule-associated protein 1 light chain 3 beta / MAP1A/MAP1B LC3 B / MAP1A/1B light chain 3 B / MAP1 light chain 3-like protein 2 / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B


Mass: 14932.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q62625
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 20% PEG 3350, 0.1M sodium citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 34039 / Num. obs: 34039 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.343 / % possible all: 69.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CY7, 1UGM

2cy7

1ugm


Resolution: 1.9→44.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 89950.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3207 9.9 %RANDOM
Rwork0.2 ---
all0.203 32304 --
obs0.203 32304 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4705 Å2 / ksol: 0.376002 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--8.77 Å20 Å2
3----9.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 184 3584
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 383 9.7 %
Rwork0.278 3552 -
obs-3935 67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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