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- PDB-5uie: Vps4-Vta1 complex -

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Basic information

Entry
Database: PDB / ID: 5uie
TitleVps4-Vta1 complex
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 (5.7 A resolution / Single particle)
AuthorsMonroe, N. / Shen, P. / Han, H. / Sundquist, W.I. / Hill, C.P.
CitationElife, 2017, 6

Elife, 2017, 6 StrPapers
Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.
Nicole Monroe / Han Han / Peter S Shen / Wesley I Sundquist / Christopher P Hill

DateDeposition: Jan 13, 2017 / Release: Apr 12, 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
F: Vacuolar protein sorting-associated protein 4
G: DOA4-independent degradation protein 4
H: Vacuolar protein sorting-associated protein VTA1
I: Vacuolar protein sorting-associated protein VTA1
J: Vacuolar protein sorting-associated protein VTA1
K: Vacuolar protein sorting-associated protein VTA1
L: Vacuolar protein sorting-associated protein VTA1
M: Vacuolar protein sorting-associated protein VTA1
N: Vacuolar protein sorting-associated protein VTA1
O: Vacuolar protein sorting-associated protein VTA1
P: Vacuolar protein sorting-associated protein VTA1
Q: Vacuolar protein sorting-associated protein VTA1
R: Vacuolar protein sorting-associated protein VTA1
S: Vacuolar protein sorting-associated protein VTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)740,84730
Polyers738,44019
Non-polymers2,40711
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)45510
ΔGint (kcal/M)-248
Surface area (A2)108920

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 18 molecules ABCDEFHIJK...

#1: Polypeptide(L)
Vacuolar protein sorting-associated protein 4 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10 / Vps4p


Mass: 48233.184 Da / Num. of mol.: 6 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P52917
#3: Polypeptide(L)
Vacuolar protein sorting-associated protein VTA1 / VPS20-associated protein 1 / Vta1p


Mass: 37359.660 Da / Num. of mol.: 12 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: Q06263

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Polypeptide(L) , 1 types, 1 molecules G

#2: Polypeptide(L)DOA4-independent degradation protein 4 / ESCRT-III complex subunit VPS2 / Vacuolar protein-sorting-associated protein 2 / Vacuolar protein-targeting protein 14 / Vps2p


Mass: 724.891 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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Non-polymers , 3 types, 11 molecules

#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


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


Mass: 66.007 Da / Num. of mol.: 3 / Formula: BeF3
#6: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Vps4-Vta1 complex / Type: COMPLEX
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3 holey carbon
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD

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Processing

SoftwareName: PHENIX / Version: 1.11_2567: / Classification: refinement
ComputingStructure refinement: PHENIX (1.11_2567: phenix.real_space_refine)
3D reconstructionResolution: 5.7 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58155
Least-squares processHighest resolution: 5.7
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610779
ELECTRON MICROSCOPYf_angle_d0.91714581
ELECTRON MICROSCOPYf_dihedral_angle_d4.4606554
ELECTRON MICROSCOPYf_chiral_restr0.0491667
ELECTRON MICROSCOPYf_plane_restr0.0071847

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