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- EMDB-42047: Cdc48-Shp1 unfolding native substrate, Class 9 -

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Basic information

Entry
Database: EMDB / ID: EMD-42047
TitleCdc48-Shp1 unfolding native substrate, Class 9
Map data
Sample
  • Complex: Cdc48-Shp1 bound to native substrate
    • Protein or peptide: Cell division control protein 48
    • Protein or peptide: Substrate
  • Ligand: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsunfoldase / AAA ATPase / p97 / CHAPERONE / Cdc48
Function / homology
Function and homology information


SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / ribophagy ...SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / ribophagy / RQC complex / DNA replication termination / mitochondria-associated ubiquitin-dependent protein catabolic process / protein-containing complex disassembly / cytoplasm protein quality control by the ubiquitin-proteasome system / positive regulation of mitochondrial fusion / HSF1 activation / nuclear protein quality control by the ubiquitin-proteasome system / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endosome to plasma membrane protein transport / protein phosphatase regulator activity / Translesion Synthesis by POLH / piecemeal microautophagy of the nucleus / mating projection tip / replisome / Protein methylation / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / ribosome-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / retrograde protein transport, ER to cytosol / KEAP1-NFE2L2 pathway / Neddylation / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / autophagosome maturation / ATP metabolic process / ERAD pathway / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / proteasome-mediated ubiquitin-dependent protein catabolic process / endoplasmic reticulum membrane / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Aspartate decarboxylase-like domain superfamily ...AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Aspartate decarboxylase-like domain superfamily / 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
Cell division control protein 48
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCooney I / Schubert HL / Cedeno K / Carson R / Fisher ON / Price JC / Hill CP / Shen PS
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133772 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170856 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112080 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG066874 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31 CA254427 United States
CitationJournal: Nat Commun / Year: 2024
Title: Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway.
Authors: Ian Cooney / Heidi L Schubert / Karina Cedeno / Olivia N Fisher / Richard Carson / John C Price / Christopher P Hill / Peter S Shen /
Abstract: The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, ...The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.
History
DepositionSep 20, 2023-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42047.png

Downloads & links

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Map

FileDownload / File: emd_42047.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 288 pix.
= 311.04 Å		1.08 Å/pix.
x 288 pix.
= 311.04 Å		1.08 Å/pix.
x 288 pix.
= 311.04 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-0.32514584 - 0.76786625
Average (Standard dev.)0.0024079855 (±0.031296205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 311.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42047_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42047_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cdc48-Shp1 bound to native substrate

EntireName: Cdc48-Shp1 bound to native substrate
Components
  • Complex: Cdc48-Shp1 bound to native substrate
    • Protein or peptide: Cell division control protein 48
    • Protein or peptide: Substrate
  • Ligand: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cdc48-Shp1 bound to native substrate

SupramoleculeName: Cdc48-Shp1 bound to native substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Cell division control protein 48

MacromoleculeName: Cell division control protein 48 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 92.106914 KDa
SequenceString: MGEEHKPLLD ASGVDPREED KTATAILRRK KKDNMLLVDD AINDDNSVIA INSNTMDKLE LFRGDTVLVK GKKRKDTVLI VLIDDELED GACRINRVVR NNLRIRLGDL VTIHPCPDIK YATRISVLPI ADTIEGITGN LFDVFLKPYF VEAYRPVRKG D HFVVRGGM ...String:
MGEEHKPLLD ASGVDPREED KTATAILRRK KKDNMLLVDD AINDDNSVIA INSNTMDKLE LFRGDTVLVK GKKRKDTVLI VLIDDELED GACRINRVVR NNLRIRLGDL VTIHPCPDIK YATRISVLPI ADTIEGITGN LFDVFLKPYF VEAYRPVRKG D HFVVRGGM RQVEFKVVDV EPEEYAVVAQ DTIIHWEGEP INREDEENNM NEVGYDDIGG CRKQMAQIRE MVELPLRHPQ LF KAIGIKP PRGVLMYGPP GTGKTLMARA VANETGAFFF LINGPEVMSK MAGESESNLR KAFEEAEKNA PAIIFIDEID SIA PKRDKT NGEVERRVVS QLLTLMDGMK ARSNVVVIAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEVLRIHTK NMKL ADDVD LEALAAETHG YVGADIASLC SEAAMQQIRE KMDLIDLDED EIDAEVLDSL GVTMDNFRFA LGNSNPSALR ETVVE SVNV TWDDVGGLDE IKEELKETVE YPVLHPDQYT KFGLSPSKGV LFYGPPGTGK TLLAKAVATE VSANFISVKG PELLSM WYG ESESNIRDIF DKARAAAPTV VFLDELDSIA KARGGSLGDA GGASDRVVNQ LLTEMDGMNA KKNVFVIGAT NRPDQID PA ILRPGRLDQL IYVPLPDENA RLSILNAQLR KTPLEPGLEL TAIAKATQGF SGADLLYIVQ RAAKYAIKDS IEAHRQHE A EKEVKVEGED VEMTDEGAKA EQEPEVDPVP YITKEHFAEA MKTAKRSVSD AELRRYEAYS QQMKASRGQF SNFNFNDAP LGTTATDNAN SNNSAPSGAG AAFGSNAEED DDLYS

UniProtKB: Cell division control protein 48

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Macromolecule #2: Substrate

MacromoleculeName: Substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.765017 KDa
SequenceString:
AAAAAAAAAA AAAVAVAVAV AAA

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Macromolecule #3: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-...

MacromoleculeName: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
type: ligand / ID: 3 / Number of copies: 7 / Formula: 08T
Molecular weightTheoretical: 492.201 Da
Chemical component information

ChemComp-08T:
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, 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 K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4690491
Startup modelType of model: OTHER / Details: Ab Initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29717
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ua1:
Cdc48-Shp1 unfolding native substrate, Class 9

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