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- PDB-5xmi: Cryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked) -

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Basic information

Entry
Database: PDB / ID: 5xmi
TitleCryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked)
ComponentsVacuolar protein sorting-associated protein 4Vacuole
KeywordsPROTEIN TRANSPORT / ATPase / EESCRTIII / Vps4
Function / homologyATPase family associated with various cellular activities (AAA) / MIT (microtubule interacting and transport) domain / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vps4 oligomerisation, C-terminal / MIT / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / AAA-protein family signature. ...ATPase family associated with various cellular activities (AAA) / MIT (microtubule interacting and transport) domain / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vps4 oligomerisation, C-terminal / MIT / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / AAA-protein family signature. / Vps4 C terminal oligomerisation domain / ESCRT IV complex / intralumenal vesicle formation / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / late endosome to vacuole transport / sterol metabolic process / macroautophagy / protein transport / protein homooligomerization / ATPase activity / endosome / protein homodimerization activity / membrane / ATP binding / identical protein binding / nucleus / Vacuolar protein sorting-associated protein 4
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsSun, S. / Li, L. / Yang, F. / Wang, X. / Fan, F. / Li, X. / Wang, H. / Sui, S.
CitationJournal: Nat Commun / Year: 2017
Title: Cryo-EM structures of the ATP-bound Vps4 hexamer and its complex with Vta1 at near-atomic resolution.
Authors: Shan Sun / Lin Li / Fan Yang / Xiaojing Wang / Fenghui Fan / Mengyi Yang / Chunlai Chen / Xueming Li / Hong-Wei Wang / Sen-Fang Sui
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 15, 2017 / Release: Aug 9, 2017

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Structure visualization

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 4
B: Vacuolar protein sorting-associated protein 4
C: Vacuolar protein sorting-associated protein 4
D: Vacuolar protein sorting-associated protein 4
E: Vacuolar protein sorting-associated protein 4
F: Vacuolar protein sorting-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,92911
Polyers289,3936
Non-polymers2,5365
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)25910
ΔGint (kcal/M)-76
Surface area (Å2)92560

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Components

#1: Protein/peptide
Vacuolar protein sorting-associated protein 4 / Vacuole / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10


Mass: 48232.199 Da / Num. of mol.: 6 / Mutation: E233Q
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10
Production host: Escherichia coli (E. coli) / References: UniProt: P52917
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vps4-E233Q hexamer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: strain ATCC 204508 / S288c
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0145 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 106918 / Symmetry type: POINT
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLStereochemistry target valuesSolvent model details
1232.884-7.51-0.42-0.55-6.310.5313.820.929HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.411840.411843.90166.3258178100.00109.6761.366MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
ELECTRON MICROSCOPY
Number of atoms included #1Total: 15000
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01915264
ELECTRON MICROSCOPYr_bond_other_d0.0010.02014628
ELECTRON MICROSCOPYr_angle_refined_deg1.1661.99520682
ELECTRON MICROSCOPYr_angle_other_deg0.8913.00033876
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.3715.0001908
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.44024.907648
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.23115.0002748
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.92615.00096
ELECTRON MICROSCOPYr_chiral_restr0.0680.2002346
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02116962
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0203144
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.33023.6747650
ELECTRON MICROSCOPYr_mcbond_other1.33023.6737649
ELECTRON MICROSCOPYr_mcangle_it2.55235.5089552
ELECTRON MICROSCOPYr_mcangle_other2.55235.5089553
ELECTRON MICROSCOPYr_scbond_it0.41123.5537614
ELECTRON MICROSCOPYr_scbond_other0.41023.5527615
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.10635.30511131
ELECTRON MICROSCOPYr_long_range_B_refined8.81628309
ELECTRON MICROSCOPYr_long_range_B_other8.81628310
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.9 Å / R factor R work: 0.559 / Lowest resolution: 4.33 Å / Number reflection R free: 0 / Number reflection R work: 4306 / Total number of bins used: 20 / Percent reflection obs: 1

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