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- PDB-4yk8: Crystal structure of the Atg101-Atg13 complex from fission yeast -

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Basic information

Entry
Database: PDB / ID: 4yk8
TitleCrystal structure of the Atg101-Atg13 complex from fission yeast
Components
  • Autophagy protein 13
  • Meiotically up-regulated gene 66 protein
KeywordsPROTEIN TRANSPORT / Autophagy / HORMA
Function / homology
Function and homology information


Macroautophagy / Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / sporulation resulting in formation of a cellular spore / autophagosome assembly / mitophagy ...Macroautophagy / Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / sporulation resulting in formation of a cellular spore / autophagosome assembly / mitophagy / autophagosome / meiotic cell cycle / macroautophagy / protein transport / protein kinase binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 101 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 101 / Autophagy-related protein 13 / Autophagy-related protein 13 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 101 / Autophagy protein 13
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsSuzuki, H. / Noda, N.N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and Technology AgencyCREST Japan
Ministry of Education, Culture, Sports, Science and Technology of Japan25111004 Japan
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation.
Authors: Suzuki, H. / Kaizuka, T. / Mizushima, N. / Noda, N.N.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiotically up-regulated gene 66 protein
B: Autophagy protein 13


Theoretical massNumber of molelcules
Total (without water)47,8812
Polymers47,8812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-12 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.822, 83.389, 91.113
Angle α, β, γ (deg.)90.00, 106.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Meiotically up-regulated gene 66 protein / Autophagy-related protein 101


Mass: 20626.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mug66, atg101, SPAC25H1.03 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O13978
#2: Protein Autophagy protein 13 / Meiotically up-regulated gene 78 protein


Mass: 27254.457 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: atg13, mug78, SPAC4F10.07c / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O36019

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 4M sodium chloride, 0.1M Tris-HCl pH 8.0, 0.2% D-fructose 1,6-diphosphate trisodium salt octahydrate, 0.2% glycerol phosphate disodium salt hydrate, 0.2% L-O-phosphoserine, 0.2% phytic acid ...Details: 4M sodium chloride, 0.1M Tris-HCl pH 8.0, 0.2% D-fructose 1,6-diphosphate trisodium salt octahydrate, 0.2% glycerol phosphate disodium salt hydrate, 0.2% L-O-phosphoserine, 0.2% phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.0000, 1.0070
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0071
ReflectionResolution: 3→43.75 Å / Num. all: 11052 / Num. obs: 11052 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.072 / Net I/σ(I): 15.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.3refinement
REFMACrefinement
Cootmodel building
PHASESphasing
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→43.74 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 3348694.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 562 5.3 %RANDOM
Rwork0.267 ---
obs0.267 10666 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.6132 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 92.3 Å2
Baniso -1Baniso -2Baniso -3
1--11.79 Å20 Å232.45 Å2
2--0.25 Å20 Å2
3---11.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.57 Å
Refinement stepCycle: 1 / Resolution: 3→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 0 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it3.022
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 74 4.2 %
Rwork0.342 1691 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION5CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top

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