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- PDB-6kbm: Crystal structure of Vac8 bound to Atg13 -

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Basic information

Entry
Database: PDB / ID: 6kbm
TitleCrystal structure of Vac8 bound to Atg13
Components
  • Autophagy-related protein 13
  • Vacuolar protein 8
KeywordsPROTEIN BINDING/PROTEIN TRANSPORT / Armadillo repeats / complex / PROTEIN BINDING-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


nucleus-vacuole junction assembly / Cvt vesicle assembly / PAS complex / Myo2p-Vac17p-Vac8p transport complex / establishment of organelle localization / regulation of cellular localization / protein localization to membrane raft / nucleus-vacuole junction / vacuole-isolation membrane contact site / armadillo repeat domain binding ...nucleus-vacuole junction assembly / Cvt vesicle assembly / PAS complex / Myo2p-Vac17p-Vac8p transport complex / establishment of organelle localization / regulation of cellular localization / protein localization to membrane raft / nucleus-vacuole junction / vacuole-isolation membrane contact site / armadillo repeat domain binding / protein targeting to vacuole involved in autophagy / vacuole inheritance / Macroautophagy / Atg1/ULK1 kinase complex / ribophagy / vacuole fusion, non-autophagic / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / protein localization to phagophore assembly site / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / pexophagy / protein-containing complex localization / protein kinase regulator activity / phagophore assembly site / fungal-type vacuole membrane / cellular response to nitrogen starvation / response to starvation / nuclear outer membrane / autophagosome assembly / mitophagy / protein-membrane adaptor activity / positive regulation of autophagy / autophagosome / macroautophagy / autophagy / lipid metabolic process / nuclear membrane / membrane raft / lipid binding / identical protein binding / membrane / cytosol
Similarity search - Function
Vacuolar protein 8 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / HORMA domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein 8 / Autophagy-related protein 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsPark, J. / Lee, C.
CitationJournal: Autophagy / Year: 2020
Title: Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.
Authors: Park, J. / Kim, H.I. / Jeong, H. / Lee, M. / Jang, S.H. / Yoon, S.Y. / Kim, H. / Park, Z.Y. / Jun, Y. / Lee, C.
History
DepositionJun 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Vacuolar protein 8
B: Autophagy-related protein 13


Theoretical massNumber of molelcules
Total (without water)69,5902
Polymers69,5902
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-9 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.727, 92.391, 139.879
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 Vacuolar protein 8


Mass: 55339.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P39968
#2: Protein Autophagy-related protein 13


Mass: 14249.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q06628
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, Tris, Ethylene glycol, PEG 3350, DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17745 / % possible obs: 95.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.27
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.435 / Num. unique obs: 794

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJG

5xjg


Resolution: 2.902→32.841 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2459 886 5 %
Rwork0.206 --
obs0.208 17726 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.902→32.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 0 44 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044102
X-RAY DIFFRACTIONf_angle_d0.8245572
X-RAY DIFFRACTIONf_dihedral_angle_d13.8371528
X-RAY DIFFRACTIONf_chiral_restr0.029673
X-RAY DIFFRACTIONf_plane_restr0.004724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9017-3.08330.36471330.30412510X-RAY DIFFRACTION87
3.0833-3.32120.30191410.2742710X-RAY DIFFRACTION93
3.3212-3.6550.26041470.23572806X-RAY DIFFRACTION97
3.655-4.1830.26611510.19552859X-RAY DIFFRACTION97
4.183-5.26660.21891530.17612901X-RAY DIFFRACTION98
5.2666-32.84310.1921610.16673054X-RAY DIFFRACTION99

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