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- EMDB-0443: Vps4 with Cyclic Peptide Bound in the Central Pore -

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Basic information

Entry
Database: EMDB / ID: EMD-0443
TitleVps4 with Cyclic Peptide Bound in the Central Pore
Map dataVps4 with Cyclic Peptide Bound in the Central Pore
Sample
  • Complex: Vps4p-Cyclic Peptide complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 4
    • Protein or peptide: Designed Cyclic Peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsVps4 / ESCRT / Vta1 / AAA ATPase / TRANSPORT PROTEIN / TRANSPORT PROTEIN-PEPTIDE complex
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 / endosomal transport / nucleus organization / ATPase complex / 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 (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHan H / Fulcher JM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P50 GM082545 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM112080 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41 GM103310 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
DepositionDec 14, 2018-
Header (metadata) releaseApr 24, 2019-
Map releaseAug 21, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0512
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0512
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ndy
  • Surface level: 0.0512
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0443.png

Downloads & links

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Map

FileDownload / File: emd_0443.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
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: 0.0512 / Movie #1: 0.0512
Minimum - Maximum-0.1273244 - 0.27742505
Average (Standard dev.)0.00059531885 (±0.0059782024)
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-0.1270.2770.001

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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
    • Protein or peptide: Vacuolar protein sorting-associated protein 4
    • Protein or peptide: Designed Cyclic Peptide
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Vps4p-Cyclic Peptide complex

SupramoleculeName: Vps4p-Cyclic Peptide complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.12075 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: QEEGEDNGGE DNKKLRGALS SAILSEKPNV KWEDVAGLEG AKEALKEAVI LPVKFPHLFK GNRKPTSGIL LYGPPGTGKS YLAKAVATE ANSTFFSVSS SDLVSKWMGE SEKLVKQLFA MARENKPSII FIDEVDALTG TRGEGESEAS RRIKTELLVQ M NGVGNDSQ ...String:
QEEGEDNGGE DNKKLRGALS SAILSEKPNV KWEDVAGLEG AKEALKEAVI LPVKFPHLFK GNRKPTSGIL LYGPPGTGKS YLAKAVATE ANSTFFSVSS SDLVSKWMGE SEKLVKQLFA MARENKPSII FIDEVDALTG TRGEGESEAS RRIKTELLVQ M NGVGNDSQ GVLVLGATNI PWQLDSAIRR RFERRIYIPL PDLAARTTMF EINVGDTPCV LTKEDYRTLG AMTEGYSGSD IA VVVKDAL MQPIRKIQSA THFKDVSTED DETRKLTPCS PGDDGAIEMS WTDIEADELK EPDLTIKDFL KAIKSTRPTV NED DLLKQE QFTRDFGQEG N

UniProtKB: Vacuolar protein sorting-associated protein 4

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Macromolecule #2: Designed Cyclic Peptide

MacromoleculeName: Designed Cyclic Peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.66004 KDa
SequenceString:
GGDEIVNKVL GGSSGG(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)GGKGCK

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / 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 #4: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / 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
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

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 237480
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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