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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 ...Vacuole) x 2
  • DOA4-independent degradation protein 4
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase
Function / homologyVta1 C-terminal domain / Vta1 like / AAA-protein family signature. / Vps4 C terminal oligomerisation domain / MIT (microtubule interacting and transport) domain / ATPase family associated with various cellular activities (AAA) / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / Vps4 oligomerisation, C-terminal ...Vta1 C-terminal domain / Vta1 like / AAA-protein family signature. / Vps4 C terminal oligomerisation domain / MIT (microtubule interacting and transport) domain / ATPase family associated with various cellular activities (AAA) / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / Vps4 oligomerisation, C-terminal / MIT / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase 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 / 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 (baker's 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
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
1.2Jul 18, 2018Structure modelData collection / Experimental preparationem_sample_support_em_sample_support.grid_type

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


Mass: 37359.660 Da / Num. of mol.: 12
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: VTA1, YLR181C / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 (baker's yeast)

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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 (baker's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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
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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