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- PDB-7ycj: Crystal structure of Vac8 bound to Vac17 -

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Basic information

Entry
Database: PDB / ID: 7ycj
TitleCrystal structure of Vac8 bound to Vac17
Components
  • Vacuolar protein 8
  • vacuole-related protein 17
KeywordsCELL CYCLE / Vacuole-inheritance
Function / homology
Function and homology information


nucleus-vacuole junction assembly / Cvt vesicle assembly / Myo2p-Vac17p-Vac8p transport complex / protein localization to membrane raft / nucleus-vacuole junction / ribophagy / vacuole inheritance / vacuole fusion, non-autophagic / pexophagy / piecemeal microautophagy of the nucleus ...nucleus-vacuole junction assembly / Cvt vesicle assembly / Myo2p-Vac17p-Vac8p transport complex / protein localization to membrane raft / nucleus-vacuole junction / ribophagy / vacuole inheritance / vacuole fusion, non-autophagic / pexophagy / piecemeal microautophagy of the nucleus / nuclear outer membrane / phagophore assembly site / fungal-type vacuole membrane / autophagosome assembly / protein-membrane adaptor activity / macroautophagy / lipid metabolic process / membrane raft / identical protein binding / membrane / cytosol
Similarity search - Function
Vacuole-related protein 17 / Vacuole-related protein 17 / Vacuolar protein 8 / 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
vacuole-related protein 17 / Vacuolar protein 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsKim, H. / Kim, H. / Lee, C.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9G8022417 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1A2C1007314 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A2C2009550 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of Vac8 bound to Vac17
Authors: Kim, H. / Park, J. / Kim, H. / Ko, N. / Park, J. / Lee, C. / Jun, Y.
History
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein 8
B: vacuole-related protein 17


Theoretical massNumber of molelcules
Total (without water)61,3322
Polymers61,3322
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-16 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.446, 147.446, 121.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Vacuolar protein 8


Mass: 55469.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VAC8, YEB3, YEL013W / Production host: Escherichia coli (E. coli) / References: UniProt: P39968
#2: Protein vacuole-related protein 17 / Vacuole-specific MYO2 receptor VAC17


Mass: 5862.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: VAC17, YCL063W, YCL63W/YCL62W / Production host: Escherichia coli (E. coli) / References: UniProt: P25591
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 25% (w/v) SOKALAN cp42, 100 mM, Tris-HCl pH 8.5, 100 mM sarcosine

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9919 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38976 / % possible obs: 99.6 % / Redundancy: 9.5 % / CC1/2: 0.999 / Net I/σ(I): 27.2
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 38976 / CC1/2: 0.365

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJG

5xjg


Resolution: 2.101→36.862 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1947 5 %
Rwork0.1875 37025 -
obs0.1893 38972 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.57 Å2 / Biso mean: 47.1867 Å2 / Biso min: 19.78 Å2
Refinement stepCycle: final / Resolution: 2.101→36.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 0 182 4279
Biso mean---48.55 -
Num. residues----536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1012-2.15370.35261360.3292257999
2.1537-2.21190.28431360.2823260499
2.2119-2.2770.30431390.24962623100
2.277-2.35050.2511360.22942597100
2.3505-2.43450.26591390.21682617100
2.4345-2.53190.27811380.20382630100
2.5319-2.64720.2471370.19012610100
2.6472-2.78670.22421390.18462628100
2.7867-2.96120.24341380.17852639100
2.9612-3.18970.2151410.18342665100
3.1897-3.51050.20231390.18862652100
3.5105-4.01790.21721410.16692681100
4.0179-5.06010.17171420.14782698100
5.0601-36.8620.20381460.1739280299
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)
11.75790.1761-0.47652.6617-0.02192.58820.11530.40690.0276-0.5022-0.1239-0.22650.46270.5557-0.02240.44990.22320.03140.54590.03580.302343.437276.471918.5235
20.6741-1.53130.27842.9129-1.261.1498-0.1738-0.01950.16010.12560.07110.0975-0.6302-0.38830.05070.52690.1092-0.1540.3263-0.05110.447647.383948.815732.7981
32.5082-0.51391.91760.2971-0.42812.2228-0.02080.1952-0.0848-0.008-0.0063-0.00740.05180.35070.02890.2757-0.0044-0.02420.255-0.01110.280777.502823.742747.0067
44.211.6376-2.93332.30640.61783.8905-0.07260.1733-0.22750.29540.0853-0.58680.03740.0633-0.36920.5169-0.1475-0.20020.6113-0.0650.592368.99629.705762.5993
53.6587-2.33981.75918.75222.15772.3358-0.01970.01660.71880.451-0.5606-0.2104-0.10180.14120.47110.4357-0.0946-0.07270.3957-0.00790.376364.046238.233745.9539
60.5655-0.3785-0.78580.45160.70721.2671-0.33180.35680.30420.9692-0.4723-1.0927-0.68920.31470.93610.8338-0.344-0.42510.7515-0.00710.86352.916457.679421.6062
74.1592-1.51184.4918.0988-1.97595.19190.32280.58460.0761-0.7223-0.96070.18270.2066-0.11650.03510.69810.3116-0.00010.5824-0.03610.308936.927579.36525.6542
86.1466-3.9513.55065.3297-0.54023.1318-0.04570.17060.801-0.1695-0.6124-0.44540.31890.41810.23030.64630.23740.06430.60770.01330.388134.133192.2822-1.0275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 139 )A14 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 264 )A140 - 264
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 515 )A265 - 515
4X-RAY DIFFRACTION4chain 'B' and (resid 289 through 294 )B289 - 294
5X-RAY DIFFRACTION5chain 'B' and (resid 295 through 304 )B295 - 304
6X-RAY DIFFRACTION6chain 'B' and (resid 305 through 331 )B305 - 331
7X-RAY DIFFRACTION7chain 'B' and (resid 332 through 339 )B332 - 339
8X-RAY DIFFRACTION8chain 'B' and (resid 340 through 344 )B340 - 344

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