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- EMDB-6736: Cryo-EM structure of ATP-bound Vps4 mutant-E233Q complex with Vta... -

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Basic information

Entry
Database: EMDB / ID: EMD-6736
TitleCryo-EM structure of ATP-bound Vps4 mutant-E233Q complex with Vta1 (unmasked)
Map data
Sample
  • Complex: Vps4-E233Q hexamer complexed with VTA1
    • Protein or peptide: Vacuolar protein sorting-associated protein 4
  • Protein or peptide: Vacuolar protein sorting-associated protein VTA1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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 / plasma membrane repair / midbody abscission / membrane fission / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / endosomal transport / ATPase complex / nucleus organization / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsSun S / Li L / Yang F / Wang X / Fan F / Li X / Wang H / Sui S
CitationJournal: Nat Commun / Year: 2017
Title: Cryo-EM structures of the ATP-bound Vps4 hexamer and its complex with Vta1 at near-atomic resolution.
Authors: Shan Sun / Lin Li / Fan Yang / Xiaojing Wang / Fenghui Fan / Mengyi Yang / Chunlai Chen / Xueming Li / Hong-Wei Wang / Sen-Fang Sui /
Abstract: The cellular ESCRT-III (endosomal sorting complex required for transport-III) and Vps4 (vacuolar protein sorting 4) comprise a common machinery that mediates a variety of membrane remodelling events. ...The cellular ESCRT-III (endosomal sorting complex required for transport-III) and Vps4 (vacuolar protein sorting 4) comprise a common machinery that mediates a variety of membrane remodelling events. Vps4 is essential for the machinery function by using the energy from ATP hydrolysis to disassemble the ESCRT-III polymer into individual proteins. Here, we report the structures of the ATP-bound Vps4 hexamer and its complex with the cofactor Vta1 (vps twenty associated 1) at resolutions of 3.9 and 4.2 Å, respectively, determined by electron cryo-microscopy. Six Vps4 subunits in both assemblies exhibit a spiral-shaped ring-like arrangement. Locating at the periphery of the hexameric ring, Vta1 dimer bridges two adjacent Vps4 subunits by two different interaction modes to promote the formation of the active Vps4 hexamer during ESCRT-III filament disassembly. The structural findings, together with the structure-guided biochemical and single-molecule analyses, provide important insights into the process of the ESCRT-III polymer disassembly by Vps4.
History
DepositionMay 15, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseAug 9, 2017-
UpdateAug 16, 2017-
Current statusAug 16, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6736.png

Downloads & links

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Map

FileDownload / File: emd_6736.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 192 pix.
= 250.856 Å		1.31 Å/pix.
x 192 pix.
= 250.856 Å		1.31 Å/pix.
x 192 pix.
= 250.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0539 / Movie #1: 0.03
Minimum - Maximum-0.07047694 - 0.13724457
Average (Standard dev.)-0.0000075093326 (±0.0067070667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 250.85568 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30654166666671.30654166666671.3065416666667
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z250.856250.856250.856
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0700.137-0.000

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Supplemental data

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Sample components

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Entire : Vps4-E233Q hexamer complexed with VTA1

EntireName: Vps4-E233Q hexamer complexed with VTA1
Components
  • Complex: Vps4-E233Q hexamer complexed with VTA1
    • Protein or peptide: Vacuolar protein sorting-associated protein 4
  • Protein or peptide: Vacuolar protein sorting-associated protein VTA1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Vps4-E233Q hexamer complexed with VTA1

SupramoleculeName: Vps4-E233Q hexamer complexed with VTA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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 S288c (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 48.232199 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 IFIDQVDALT GT RGEGESE ASRRIKTELL VQMNGVGNDS QGVLVLGATN IPWQLDSAIR RRFERRIYIP LPDLAARTTM FEINVGDTPC VLT KEDYRT LGAMTEGYSG SDIAVVVKDA LMQPIRKIQS ATHFKDVSTE DDETRKLTPC SPGDDGAIEM SWTDIEADEL KEPD LTIKD FLKAIKSTRP TVNEDDLLKQ EQFTRDFGQE GN

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Macromolecule #2: Vacuolar protein sorting-associated protein VTA1

MacromoleculeName: Vacuolar protein sorting-associated protein VTA1 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 37.35966 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157109
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION

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