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

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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 dataVps4-Vta1 complex
Sample
  • Complex: Vps4-Vta1 complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 4,Protein hcp1
    • Protein or peptide: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2
    • 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 / Macroautophagy / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via 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 / Macroautophagy / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / ATP export / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / midbody abscission / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / reticulophagy / endosomal transport / lipid transport / ATPase complex / nucleus organization / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / midbody / protein-macromolecule adaptor activity / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / 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 ...: / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / 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 / Snf7 family / Snf7 / 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
DOA4-independent degradation protein 4 / Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein VTA1 / Protein hcp1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer'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
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.
History
DepositionAug 16, 2017-
Header (metadata) releaseSep 6, 2017-
Map releaseDec 6, 2017-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing 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

emd_8887.png

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)
AnnotationVps4-Vta1 complex
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

Histogram

Histogram (log scale)
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
Components
  • Complex: Vps4-Vta1 complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 4,Protein hcp1
    • Protein or peptide: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2
    • 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,Protein hcp1

MacromoleculeName: Vacuolar protein sorting-associated protein 4,Protein hcp1
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: 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
Molecular weightTheoretical: 55.768402 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF KGNRKPTSGI LLYGPPGTGK SYLAKAVAT EANSTFFSVS SSDLVSKWMG ESEKLVKQLF AMARENKPSI IFIDEVDALT GTRGEGESEA SRRIKTELLV Q MNGVGNDS ...String:
GQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF KGNRKPTSGI LLYGPPGTGK SYLAKAVAT EANSTFFSVS SSDLVSKWMG ESEKLVKQLF AMARENKPSI IFIDEVDALT GTRGEGESEA SRRIKTELLV Q MNGVGNDS QGVLVLGATN IPWQLDSAIR RRFERRIYIP LPDLAARTTM FEINVGDTPC VLTKEDYRTL GAMTEGYSGS DI AVVVKDA LMQPIRKIQS ATHFKDVSTE DDETRKLTPC SPGDDGAIEM SWTDIEADEL KEPDLTIKDF LKAIKSTRPT VNE DDLLKQ EQFTRDFGQE GNGGGGSGGG GSGGGGSGGG MAVDMFIKIG DVKGESKDKT HAEEIDVLAW SWGMSQSGSM HMGG GGGAG KVNVQDLSFT KYIDKSTPNL MMACSSGKHY PQAKLTIRKA GGENQVEYLI ITLKEVLVSS VSTGGSGGED RLTEN VTLN FAQVQVDYQP QKADGAKDGG PVKYGWNIRQ NVQAG

UniProtKB: Vacuolar protein sorting-associated protein 4, Protein hcp1

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Macromolecule #2: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2

MacromoleculeName: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 954.122 Da
SequenceString:
(ACE)DEIVNKVL(NH2)

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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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 37.35966 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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: 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
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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.25 sec. / Average electron dose: 1.55 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: e2initialmodel.py
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 82225
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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