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- EMDB-8549: Vps4-Vta1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-8549
TitleVps4-Vta1 complex
Map dataVps4-Vta1 complex
Sample
  • Complex: Vps4-Vta1 complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 4
    • Protein or peptide: DOA4-independent degradation protein 4
    • Protein or peptide: Vacuolar protein sorting-associated protein VTA1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsVps4 / ESCRT / Vta1 / AAA ATPase / TRANSPORT PROTEIN
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 / midbody abscission ...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 / midbody abscission / multivesicular body sorting pathway / vacuole organization / plasma membrane repair / membrane fission / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / lipid transport / endosomal transport / nucleus organization / ATPase complex / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / protein-macromolecule adaptor activity / midbody / 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: 5.7 Å
AuthorsMonroe N / Shen P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 GM082545 United States
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.
History
DepositionJan 13, 2017-
Header (metadata) releaseFeb 8, 2017-
Map releaseApr 12, 2017-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0222
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0222
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5uie
  • Surface level: 0.0222
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8549.png

Downloads & links

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Map

FileDownload / File: emd_8549.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVps4-Vta1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 138 pix.
= 194.442 Å		1.41 Å/pix.
x 138 pix.
= 194.442 Å		1.41 Å/pix.
x 138 pix.
= 194.442 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.409 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0222 / Movie #1: 0.0222
Minimum - Maximum-0.016907765 - 0.066737935
Average (Standard dev.)-0.0011521827 (±0.005928796)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS138138138
D min/max/mean-0.0170.067-0.001

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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: Vacuolar protein sorting-associated protein 4
    • Protein or peptide: DOA4-independent degradation protein 4
    • Protein or peptide: Vacuolar protein sorting-associated protein VTA1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Vps4-Vta1 complex

SupramoleculeName: Vps4-Vta1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Vacuolar protein sorting-associated protein 4

MacromoleculeName: Vacuolar protein sorting-associated protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.233184 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSTGDFLTKG IELVQKAIDL DTATQYEEAY TAYYNGLDYL MLALKYEKNP KSKDLIRAKF TEYLNRAEQL KKHLESEEAN AAKKSPSAG SGSNGGNKKI SQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF K GNRKPTSG ...String:
MSTGDFLTKG IELVQKAIDL DTATQYEEAY TAYYNGLDYL MLALKYEKNP KSKDLIRAKF TEYLNRAEQL KKHLESEEAN AAKKSPSAG SGSNGGNKKI SQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF K GNRKPTSG ILLYGPPGTG KSYLAKAVAT EANSTFFSVS SSDLVSKWMG ESEKLVKQLF AMARENKPSI IFIDEVDALT GT RGEGESE ASRRIKTELL VQMNGVGNDS QGVLVLGATN IPWQLDSAIR RRFERRIYIP LPDLAARTTM FEINVGDTPC VLT KEDYRT LGAMTEGYSG SDIAVVVKDA LMQPIRKIQS ATHFKDVSTE DDETRKLTPC SPGDDGAIEM SWTDIEADEL KEPD LTIKD FLKAIKSTRP TVNEDDLLKQ EQFTRDFGQE GN

UniProtKB: Vacuolar protein sorting-associated protein 4

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Macromolecule #2: DOA4-independent degradation protein 4

MacromoleculeName: DOA4-independent degradation protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 724.891 Da
SequenceString:
(ACE)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Vacuolar protein sorting-associated protein VTA1

MacromoleculeName: Vacuolar protein sorting-associated protein VTA1 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.35966 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKA KIYMLNFTMS LYNEKLKQLK DGPWDVMLKR SLWCCIDLFS CILHLWKENI SETSTNSLQK RIKYCKIYLS K LAKGEIGS ...String:
MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKA KIYMLNFTMS LYNEKLKQLK DGPWDVMLKR SLWCCIDLFS CILHLWKENI SETSTNSLQK RIKYCKIYLS K LAKGEIGS SDEKTLDYAD FADDSEEIKD EDVDHQTSDL ENNNNDKVEG LAPKDQTTSY EPVDEVPEFI DDADSVNEEE QT VDKNEDA ITKDEQQVVK KEVDLTRPSA PSEPAAAEHK SYTKDELTKI MDRASKIEQI QKLAKYAISA LNYEDLPTAK DEL TKALDL LNSI

UniProtKB: Vacuolar protein sorting-associated protein VTA1

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 58155
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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