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- EMDB-8887: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-8887
TitleVps4p-Vta1p complex with peptide binding to the central pore of Vps4p
Map data
SampleVps4-Vta1 complex
  • (Vacuolar protein sorting-associated protein ...Vacuole) x 2
  • ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2
  • (ligand) x 3
Function / homology
Function and homology information


ESCRT IV complex / ESCRT III complex / intralumenal vesicle formation / endosome transport via multivesicular body sorting pathway / ATP export / protein retention in Golgi apparatus / vacuole organization / late endosome to vacuole transport via multivesicular body sorting pathway / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport ...ESCRT IV complex / ESCRT III complex / intralumenal vesicle formation / endosome transport via multivesicular body sorting pathway / ATP export / protein retention in Golgi apparatus / vacuole organization / late endosome to vacuole transport via multivesicular body sorting pathway / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport / sterol metabolic process / reticulophagy / ATPase activator activity / lipid transport / multivesicular body / protein-macromolecule adaptor activity / macroautophagy / protein transport / endosome / ATPase activity / endoplasmic reticulum / protein homodimerization activity / membrane / extracellular region / ATP binding / identical protein binding / nucleus / cytoplasm
Type VI secretion system effector Hcp / ATPase, AAA-type, core / Vacuolar protein sorting-associated protein IST1-like / Vta1, C-terminal / Vta1/callose synthase, N-terminal / Hcp1-like superfamily / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / Vps4 oligomerisation, C-terminal ...Type VI secretion system effector Hcp / ATPase, AAA-type, core / Vacuolar protein sorting-associated protein IST1-like / Vta1, C-terminal / Vta1/callose synthase, N-terminal / Hcp1-like superfamily / MIT domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Vacuolar protein sorting-associate protein Vta1/Callose synthase, N-terminal / Vps4 oligomerisation, C-terminal / AAA+ ATPase domain / MIT / Snf7 family / ATPase, AAA-type, conserved site
DOA4-independent degradation protein 4 / Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein VTA1 / Protein hcp1
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHan H / Monroe N / Shen P / Sundquist WI / Hill CP
CitationJournal: Elife / Year: 2017
Title: The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Authors: Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill /
Abstract: The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now ...The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a 'conveyor belt' model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end.
Validation ReportPDB-ID: 6ap1

SummaryFull report
PDB-ID: 6bmf

SummaryFull report
About validation report
History
DepositionAug 16, 2017-
Header (metadata) releaseSep 6, 2017-
Map releaseDec 6, 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: 0.0749
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0749
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ap1
  • Surface level: 0.0749
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6bmf
  • Surface level: 0.0749
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8887.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 280.602 Å
1.1 Å/pix.
x 256 pix.
= 280.602 Å
1.1 Å/pix.
x 256 pix.
= 280.602 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density
Contour LevelBy AUTHOR: 0.0749 / Movie #1: 0.0749
Minimum - Maximum-0.19472791 - 0.38840204
Average (Standard dev.)0.0004073913 (±0.0066645136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.6016 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09610156251.09610156251.0961015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z280.602280.602280.602
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1950.3880.000

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Supplemental data

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Sample components

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Entire Vps4-Vta1 complex

EntireName: Vps4-Vta1 complex / Number of components: 7

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Component #1: protein, Vps4-Vta1 complex

ProteinName: Vps4-Vta1 complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #2: protein, Vacuolar protein sorting-associated protein 4,Protein hcp1

ProteinName: Vacuolar protein sorting-associated protein 4,Protein hcp1Vacuole
Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 55.768402 kDa
SourceSpecies: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #3: protein, ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2

ProteinName: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.954122 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, Vacuolar protein sorting-associated protein VTA1

ProteinName: Vacuolar protein sorting-associated protein VTA1Vacuole
Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 37.35966 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #5: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #6: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.600705 MDa

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.55 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 82225
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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