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- EMDB-20141: Vps4 with Cyclic Peptide Bound in the Central Pore (Focused Class... -

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Basic information

Entry
Database: EMDB / ID: EMD-20141
TitleVps4 with Cyclic Peptide Bound in the Central Pore (Focused Classification of Subunit F, State3)
Map dataVps4 with Cyclic Peptide Bound in the Central Pore (Focused Classification of Subunit F, State3)
Sample
  • Complex: Vps4p-Cyclic Peptide complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsHan H / Fulcher JM / Shen PS / Hill CP
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteP50 GM082545 United States
National Institutes of Health/National Human Genome Research InstituteP41 GM103310 United States
National Institutes of Health/National Human Genome Research InstituteR01 GM112080 United States
CitationJournal: Elife / Year: 2019
Title: Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.
Authors: Han Han / James M Fulcher / Venkata P Dandey / Janet H Iwasa / Wesley I Sundquist / Michael S Kay / Peter S Shen / Christopher P Hill /
Abstract: Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single ...Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains.
History
DepositionApr 22, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseAug 21, 2019-
UpdateAug 21, 2019-
Current statusAug 21, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20141.png

Downloads & links

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Map

FileDownload / File: emd_20141.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVps4 with Cyclic Peptide Bound in the Central Pore (Focused Classification of Subunit F, State3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0205 / Movie #1: 0.0205
Minimum - Maximum-0.013873965 - 0.05465349
Average (Standard dev.)-0.000009061909 (±0.0027000108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0140.055-0.000

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Supplemental data

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Sample components

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Entire : Vps4p-Cyclic Peptide complex

EntireName: Vps4p-Cyclic Peptide complex
Components
  • Complex: Vps4p-Cyclic Peptide complex

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Supramolecule #1: Vps4p-Cyclic Peptide complex

SupramoleculeName: Vps4p-Cyclic Peptide complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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 #1

Preparation ID1
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: SPOTITON

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Sample preparation #2

Preparation ID2
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: SPOTITON

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Digitization - Frames/image: 2-50 / Average exposure time: 0.2 sec. / Average electron dose: 1.5336 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 14000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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