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- EMDB-20149: Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) -

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Basic information

Entry
Database: EMDB / ID: EMD-20149
TitleCdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)
Map dataCdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)
Sample
  • Complex: Cdc48-Substrate Complex
    • Protein or peptide: Cell division control protein 48
    • Protein or peptide: Substrate bound to the central pore of the Cdc48 hexamer
    • Protein or peptide: UBX domain-containing protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsCdc48 / AAA+ ATPase / substrate translocation / MOTOR PROTEIN
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 / ascospore formation / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation ...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 / ascospore formation / 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 / nuclear membrane reassembly / 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 / K48-linked polyubiquitin modification-dependent protein binding / glycogen metabolic process / KEAP1-NFE2L2 pathway / Neddylation / protein quality control for misfolded or incompletely synthesized proteins / Golgi organization / autophagosome assembly / 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 / membrane fusion / endoplasmic reticulum membrane / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain ...SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / 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 / Ubiquitin-like domain superfamily / 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 / UBX domain-containing protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsCooney I / Han H / Stewart M / Carson RH / Hansen D / Price JC / Hill CP / Shen PS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P50GM082545 United States
CitationJournal: Science / Year: 2019
Title: Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.
Authors: Ian Cooney / Han Han / Michael G Stewart / Richard H Carson / Daniel T Hansen / Janet H Iwasa / John C Price / Christopher P Hill / Peter S Shen /
Abstract: The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite ...The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom-resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases.
History
DepositionApr 24, 2019-
Header (metadata) releaseMay 8, 2019-
Map releaseJul 10, 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: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6opc
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20149.png

Downloads & links

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Map

FileDownload / File: emd_20149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 256 pix.
= 299.008 Å		1.17 Å/pix.
x 256 pix.
= 299.008 Å		1.17 Å/pix.
x 256 pix.
= 299.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.168 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0056 / Movie #1: 0.008
Minimum - Maximum-0.027789509 - 0.06803693
Average (Standard dev.)0.000003440544 (±0.0025505817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 299.008 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1681.1681.168
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z299.008299.008299.008
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0280.0680.000

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Supplemental data

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Sample components

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Entire : Cdc48-Substrate Complex

EntireName: Cdc48-Substrate Complex
Components
  • Complex: Cdc48-Substrate Complex
    • Protein or peptide: Cell division control protein 48
    • Protein or peptide: Substrate bound to the central pore of the Cdc48 hexamer
    • Protein or peptide: UBX domain-containing protein 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cdc48-Substrate Complex

SupramoleculeName: Cdc48-Substrate 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: 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 bound to the central pore of the Cdc48 hexamer

MacromoleculeName: Substrate bound to the central pore of the Cdc48 hexamer
type: protein_or_peptide / ID: 2 / Details: co-purified with Cdc48 hexamer / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.890321 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #3: UBX domain-containing protein 1

MacromoleculeName: UBX domain-containing protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.041105 KDa
SequenceString: MAEIPDETIQ QFMALTNVSH NIAVQYLSEF GDLNEALNSY YASQTDDQKD RREEAHWNRQ QEKALKQEAF STNSSNKAIN TEHVGGLCP KPGSSQGSNE YLKRKGSTSP EPTKGSSRSG SGNNSRFMSF SDMVRGQADD DDEDQPRNTF AGGETSGLEV T DPSDPNSL ...String:
MAEIPDETIQ QFMALTNVSH NIAVQYLSEF GDLNEALNSY YASQTDDQKD RREEAHWNRQ QEKALKQEAF STNSSNKAIN TEHVGGLCP KPGSSQGSNE YLKRKGSTSP EPTKGSSRSG SGNNSRFMSF SDMVRGQADD DDEDQPRNTF AGGETSGLEV T DPSDPNSL LKDLLEKARR GGQMGAENGF RDDEDHEMGA NRFTGRGFRL GSTIDAADEV VEDNTSQSQR RPEKVTREIT FW KEGFQVA DGPLYRYDDP ANSFYLSELN QGRAPLKLLD VQFGQEVEVN VYKKLDESYK APTRKLGGFS GQGQRLGSPI PGE SSPAEV PKNETPAAQE QPMPDNEPKQ GDTSIQIRYA NGKREVLHCN STDTVKFLYE HVTSNANTDP SRNFTLNYAF PIKP ISNDE TTLKDADLLN SVVVQRWA

UniProtKB: UBX domain-containing protein 1

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 10 / 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: 8 / 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: 8 / 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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54367
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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