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- PDB-6bmf: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -

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Basic information

Entry
Database: PDB / ID: 6bmf
TitleVps4p-Vta1p complex with peptide binding to the central pore of Vps4p
DescriptorVacuolar protein sorting-associated protein 4
DOA4-independent degradation protein 4
Vacuolar protein sorting-associated protein VTA1
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsHan, H. / Monroe, N. / Shen, P. / Sundquist, W.I. / Hill, C.P.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2017 / Release: Dec 6, 2017

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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
G: Vps2p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,98918
Polyers186,5586
Non-polymers2,43112
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)21770
ΔGint (kcal/M)-108
Surface area (Å2)61180

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Components

#1: Polypeptide(L)
Vacuolar protein sorting-associated protein 4 / Vps4 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10


Mass: 37120.750 Da / Num. of mol.: 5 / Fragment: UNP residues 101-437
Source: (gene. exp.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
References: UniProt: P52917
#2: Polypeptide(L)Vps2p


Mass: 954.122 Da / Num. of mol.: 1
Source: (synth.) Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2
#4: ChemicalChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Formula: BeF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Vps4p-Vps2p complex / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae
Source (recombinant)Organism: Escherichia coli BL21(DE3)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 2-40

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategoryImage processing ID
10RELIONINITIAL EULER ASSIGNMENT1
11RELIONFINAL EULER ASSIGNMENT1
13RELIONRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 82225 / Symmetry type: POINT
Least-squares processHighest resolution: 3.2 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01812700
ELECTRON MICROSCOPYf_angle_d1.55317171
ELECTRON MICROSCOPYf_dihedral_angle_d5.9137740
ELECTRON MICROSCOPYf_chiral_restr0.0781949
ELECTRON MICROSCOPYf_plane_restr0.0112197

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