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- PDB-6kbn: Crystal structure of Vac8 (del 19-33) bound to Atg13 -

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Basic information

Entry
Database: PDB / ID: 6kbn
TitleCrystal structure of Vac8 (del 19-33) 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 / protein localization to membrane raft / establishment of organelle localization / regulation of cellular localization / 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 / protein localization to membrane raft / establishment of organelle localization / regulation of cellular localization / nucleus-vacuole junction / vacuole-isolation membrane contact site / armadillo repeat domain binding / protein targeting to vacuole involved in autophagy / vacuole inheritance / vacuole fusion, non-autophagic / Atg1/ULK1 kinase complex / Macroautophagy / ribophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / pexophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / protein-containing complex localization / protein kinase regulator activity / fungal-type vacuole membrane / nuclear outer membrane / phagophore assembly site / cellular response to nitrogen starvation / autophagy of mitochondrion / response to starvation / autophagosome assembly / mitophagy / positive regulation of autophagy / protein-membrane adaptor activity / autophagosome / macroautophagy / lipid metabolic process / autophagy / 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: 3.2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,8534
Polymers151,8534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SAXS, cross-linking, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-22 kcal/mol
Surface area46270 Å2
Unit cell
Length a, b, c (Å)69.475, 85.268, 272.820
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: 61676.777 Da / Num. of mol.: 2 / Mutation: residues 19-33 deletion
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.: 2
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

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, N-(2-Acetamido)iminodiacetic acid, Ammonium sulfate

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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: 3.2→50 Å / Num. obs: 27903 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 17.88
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 1320

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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: 3.2→35.113 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.96
RfactorNum. reflection% reflection
Rfree0.2546 1394 5 %
Rwork0.2163 --
obs0.2182 27864 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→35.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 0 0 8069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088178
X-RAY DIFFRACTIONf_angle_d1.66711091
X-RAY DIFFRACTIONf_dihedral_angle_d15.8593060
X-RAY DIFFRACTIONf_chiral_restr0.0681338
X-RAY DIFFRACTIONf_plane_restr0.0071436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1579-3.27060.3531120.31562127X-RAY DIFFRACTION80
3.2706-3.40150.30481380.32623X-RAY DIFFRACTION98
3.4015-3.55620.3381400.27362655X-RAY DIFFRACTION99
3.5562-3.74350.25591390.24112655X-RAY DIFFRACTION99
3.7435-3.97770.27431420.21942677X-RAY DIFFRACTION99
3.9777-4.28430.26331400.19662685X-RAY DIFFRACTION99
4.2843-4.71460.20971420.18442683X-RAY DIFFRACTION99
4.7146-5.39460.22461440.19812732X-RAY DIFFRACTION99
5.3946-6.78860.26641440.24812740X-RAY DIFFRACTION99
6.7886-35.11520.2261530.17842893X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7309-0.0057-1.05112.4855-1.91873.7134-0.1628-0.22740.2347-0.02680.0262-0.1312-0.06650.10480.10390.31880.0115-0.12290.231-0.08570.5217101.2621172.374280.3539
24.1330.4243-0.16922.20790.16233.8435-0.2874-0.49650.235-0.2267-0.6168-0.23430.60090.02180.72270.6565-0.0774-0.03930.2542-0.03840.7533104.5957172.4845272.2513
30.9342-0.1061-0.5981.3967-1.26734.5235-0.2454-0.4932-0.2240.34320.29550.3391-0.2261-1.0011-0.05010.54410.2377-0.06461.0275-0.0190.7419122.3748189.9096179.3094
40.521.17920.09532.6403-0.22351.3965-0.8962-0.6026-0.4473-0.2511-0.13710.19110.5635-0.19371.04460.58990.18320.12631.96130.12650.9268122.6169187.5657188.4526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 47 through 576)
2X-RAY DIFFRACTION2(chain 'B' and resid 665 through 685)
3X-RAY DIFFRACTION3(chain 'C' and resid 48 through 578)
4X-RAY DIFFRACTION4(chain 'D' and resid 665 through 685)

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