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- EMDB-8570: Vps4-Vta1 complex, State 3 of subunitF -

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Basic information

Entry
Database: EMDB / ID: EMD-8570
TitleVps4-Vta1 complex, State 3 of subunitF
Map dataVps4-Vta1 complex, State 3 of subunitF
Sample
  • Complex: Vps4-vta1 complex
    • Protein or peptide: Vps4p
    • Protein or peptide: Vta1p
    • Protein or peptide: Vps2p
Function / homology
Function and homology information


ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / multivesicular body sorting pathway ...ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / midbody abscission / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / endosomal transport / lipid transport / ATPase complex / nucleus organization / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / midbody / protein-macromolecule adaptor activity / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal ...Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein VTA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsMonroe N / Shen P / Han H / Sundquist WI / Hill CP
CitationJournal: To be Published
Title: Peptide translocation by Vps4-Vta1 complex
Authors: Monroe N / Shen P / Han H / Sundquist WI / Hill CP
History
DepositionJan 20, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseApr 12, 2017-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_8570.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVps4-Vta1 complex, State 3 of subunitF
Voxel sizeX=Y=Z: 1.409 Å
Density
Contour LevelBy AUTHOR: 0.0212 / Movie #1: 0.024
Minimum - Maximum-0.018915841 - 0.061387718
Average (Standard dev.)-0.0011124294 (±0.006188263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions138138138
Spacing138138138
CellA=B=C: 194.442 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4091.4091.409
M x/y/z138138138
origin x/y/z0.0000.0000.000
length x/y/z194.442194.442194.442
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS138138138
D min/max/mean-0.0190.061-0.001

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Supplemental data

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Sample components

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Entire : Vps4-vta1 complex

EntireName: Vps4-vta1 complex
Components
  • Complex: Vps4-vta1 complex
    • Protein or peptide: Vps4p
    • Protein or peptide: Vta1p
    • Protein or peptide: Vps2p

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Supramolecule #1: Vps4-vta1 complex

SupramoleculeName: Vps4-vta1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Vps4p

MacromoleculeName: Vps4p / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF KGNRKPTSGI LLYGPPGTGK SYLAKAVATE ANSTFFSVSS SDLVSKWMGE SEKLVKQLFA MARENKPSII FIDEVDALTG TRGEGESEAS RRIKTELLVQ MNGVGNDSQG ...String:
GQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF KGNRKPTSGI LLYGPPGTGK SYLAKAVATE ANSTFFSVSS SDLVSKWMGE SEKLVKQLFA MARENKPSII FIDEVDALTG TRGEGESEAS RRIKTELLVQ MNGVGNDSQG VLVLGATNIP WQLDSAIRRR FERRIYIPLP DLAARTTMFE INVGDTPCVL TKEDYRTLGA MTEGYSGSDI AVVVKDALMQ PIRKIQSATH FKDVSTEDDE TRKLTPCSPG DDGAIEMSWT DIEADELKEP DLTIKDFLKA IKSTRPTVNE DDLLKQEQFT RDFGQEGN

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Macromolecule #2: Vta1p

MacromoleculeName: Vta1p / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GTKDELTKIM DRASKIEQIQ KLAKYAISAL NYEDLPTAKD ELTKALDLLN SI

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Macromolecule #3: Vps2p

MacromoleculeName: Vps2p / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
DEIVNKVL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.2 sec. / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / Details: e2initialmodel.py
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 38421
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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