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- PDB-5xjg: Crystal structure of Vac8p bound to Nvj1p -

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Basic information

Entry
Database: PDB / ID: 5xjg
TitleCrystal structure of Vac8p bound to Nvj1p
Components
  • Nucleus-vacuole junction protein 1
  • Vacuolar protein 8Vacuole
KeywordsSIGNALING PROTEIN/MEMBRANE PROTEIN / Vac8p / Nvj1p / Membrane contact site / Nucleus-vacuole junction / SIGNALING PROTEIN-MEMBRANE PROTEIN complex
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 / fungal-type vacuole membrane / phagophore assembly site / nuclear outer membrane / autophagosome assembly / protein-membrane adaptor activity / nuclear periphery / macroautophagy / protein localization / lipid metabolic process / nuclear envelope / membrane raft / membrane / identical protein binding / cytosol
Similarity search - Function
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
Nucleus-vacuole junction protein 1 / Vacuolar protein 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsJeong, H. / Park, J. / Jun, Y. / Lee, C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Mechanistic insight into the nucleus-vacuole junction based on the Vac8p-Nvj1p crystal structure.
Authors: Jeong, H. / Park, J. / Kim, H.I. / Lee, M. / Ko, Y.J. / Lee, S. / Jun, Y. / Lee, C.
History
DepositionMay 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Nucleus-vacuole junction protein 1
C: Vacuolar protein 8
D: Nucleus-vacuole junction protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,3427
Polymers131,2624
Non-polymers1,0793
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-26 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.082, 115.630, 84.131
Angle α, β, γ (deg.)90.00, 114.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar protein 8 / Vacuole


Mass: 55339.992 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 10-515
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VAC8, YEB3, YEL013W / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P39968
#2: Protein Nucleus-vacuole junction protein 1


Mass: 10291.191 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 229-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NVJ1, VAB36, YHR195W / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P38881
#3: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C18H38O9 / Comment: precipitant*YM
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, BTP, t-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 57806 / % possible obs: 98.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.595 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 2016 3.54 %
Rwork0.1896 --
obs0.1907 57022 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7978 0 53 181 8212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048132
X-RAY DIFFRACTIONf_angle_d0.90811023
X-RAY DIFFRACTIONf_dihedral_angle_d14.0113044
X-RAY DIFFRACTIONf_chiral_restr0.0321332
X-RAY DIFFRACTIONf_plane_restr0.0041420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.22761420.17343920X-RAY DIFFRACTION100
2.46-2.52650.23921410.17493870X-RAY DIFFRACTION100
2.5265-2.60080.19721390.1763903X-RAY DIFFRACTION100
2.6008-2.68470.22241460.17743910X-RAY DIFFRACTION100
2.6847-2.78060.2071450.17433926X-RAY DIFFRACTION100
2.7806-2.89180.22141460.18223933X-RAY DIFFRACTION100
2.8918-3.02330.2241450.19173909X-RAY DIFFRACTION100
3.0233-3.18250.23821420.20073921X-RAY DIFFRACTION100
3.1825-3.38160.23891490.21823968X-RAY DIFFRACTION100
3.3816-3.64230.24061420.2073917X-RAY DIFFRACTION100
3.6423-4.0080.221460.18253931X-RAY DIFFRACTION100
4.008-4.58620.20461460.17853923X-RAY DIFFRACTION100
4.5862-5.77110.20291410.19733976X-RAY DIFFRACTION100
5.7711-29.5970.23571460.18753999X-RAY DIFFRACTION99

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