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- PDB-5uie: Vps4-Vta1 complex -

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Basic information

Entry
Database: PDB / ID: 5uie
TitleVps4-Vta1 complex
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • DOA4-independent degradation protein 4
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase
Function / homologyVta1 like / P-loop containing nucleoside triphosphate hydrolase / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / MIT / Vps4 oligomerisation, C-terminal / Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / MIT domain superfamily / ATPase family associated with various cellular activities (AAA) ...Vta1 like / P-loop containing nucleoside triphosphate hydrolase / AAA+ ATPase domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / MIT / Vps4 oligomerisation, C-terminal / Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / MIT domain superfamily / ATPase family associated with various cellular activities (AAA) / MIT (microtubule interacting and transport) domain / Vps4 C terminal oligomerisation domain / AAA-protein family signature. / ESCRT IV complex / intralumenal vesicle formation / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / vacuole organization / late endosome to vacuole transport / ATPase activator activity / sterol metabolic process / lipid transport / positive regulation of protein oligomerization / multivesicular body / macroautophagy / protein transport / protein homooligomerization / ATPase activity / endosome / protein homodimerization activity / membrane / ATP binding / identical protein binding / nucleus / Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein VTA1
Function and homology information
Specimen sourceSaccharomyces cerevisiae / Yeast / yeast /
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.7 Å resolution
AuthorsMonroe, N. / Shen, P. / Han, H. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Elife / Year: 2017
Title: Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase.
Authors: Nicole Monroe / Han Han / Peter S Shen / Wesley I Sundquist / Christopher P Hill
Abstract: Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM ...Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP·BeF, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating. The final Vps4 subunit completes a notched-washer configuration as if transitioning between the ends of the helix. We propose that ATP binding propagates growth at one end of the helix while hydrolysis promotes disassembly at the other end, so that Vps4 'walks' along ESCRT-III until it encounters the ordered N-terminal domain to destabilize the ESCRT-III lattice. This model may be generally applicable to other protein-translocating AAA ATPases.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 13, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Sep 13, 2017Structure modelAuthor supporting evidence / Data collectionem_image_scans / pdbx_audit_support_pdbx_audit_support.funding_organization

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Structure visualization

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Structure viewerMolecule:
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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 (Å2)45510
ΔGint (kcal/M)-248
Surface area (Å2)108920

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Components

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

#1: Protein/peptide
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
Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10
Production host: Escherichia coli BL21(DE3) / References: UniProt:P52917
#3: Protein/peptide
Vacuolar protein sorting-associated protein VTA1 / VPS20-associated protein 1 / Vta1p


Mass: 37359.660 Da / Num. of mol.: 12 / Source: (gene. exp.) Saccharomyces cerevisiae / Gene: VTA1, YLR181C / Production host: Escherichia coli BL21(DE3) / References: UniProt:Q06263

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Protein/peptide , 1 types, 1 molecules G

#2: Protein/peptide 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


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


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

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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-Vta1 complex / Type: COMPLEX / Entity ID: 1,2,3,4,5,6 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
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
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 % / Chamber temperature: 277 kelvins

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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 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11_2567: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58155 / Symmetry type: POINT
Least-squares processHighest resolution: 5.7 Å
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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