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- EMDB-27273: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in t... -

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Entry
Database: EMDB / ID: EMD-27273
TitleSaccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP
Map datacomposite map of substrate unbound class of particles. This class represents the portion of particles where Ufd1/Npl4/Cdc48 was not bound to the SUMO-ubiquitin(K48polyUb)-mEOS substrate. Composite map represents the composite map of overall and focused refinements under this deposition.
Sample
  • Complex: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP
    • Complex: Cdc48 hexamer
      • Protein or peptide: Cell division control protein 48
    • Complex: Ufd1/Npl4 tower
      • Protein or peptide: Nuclear protein localization protein 4
      • Protein or peptide: Ubiquitin fusion degradation protein 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
KeywordsATPASE / ATPASE COMPLEX / UBIQUITIN / SUMO / SMT3 / QUALITY CONTROL / MOTOR PROTEIN
Function / homology
Function and homology information


SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / sister chromatid biorientation / protein localization to vacuole / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum membrane fusion ...SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / sister chromatid biorientation / protein localization to vacuole / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum membrane fusion / ribophagy / DNA replication termination / RQC complex / mitochondria-associated ubiquitin-dependent protein catabolic process / positive regulation of mitochondrial fusion / cytoplasm protein quality control by the ubiquitin-proteasome system / HSF1 activation / nuclear protein quality control by the ubiquitin-proteasome system / protein-containing complex disassembly / 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 / Protein methylation / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / replisome / ribosome-associated ubiquitin-dependent protein catabolic process / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / retrograde protein transport, ER to cytosol / nonfunctional rRNA decay / KEAP1-NFE2L2 pathway / Neddylation / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / autophagosome maturation / mRNA transport / ATP metabolic process / ERAD pathway / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 ...Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / 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 / MPN domain / MPN domain profile. / 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 / Nuclear protein localization protein 4 / Ubiquitin fusion degradation protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLee HG / Lima CD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118080 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
Authors: Hyein G Lee / Abigail A Lemmon / Christopher D Lima /
Abstract: The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets ...The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets are established; however, prior studies suggest that the complex also targets substrates modified by the ubiquitin-like protein SUMO. Here, we show that interactions between Ufd1 and SUMO enhance unfolding of substrates modified by SUMO-polyubiquitin hybrid chains by the budding yeast Ufd1/Npl4/Cdc48 complex compared to substrates modified by polyubiquitin chains, a difference that is accentuated when the complex has a choice between these substrates. Incubating Ufd1/Npl4/Cdc48 with a substrate modified by a SUMO-polyubiquitin hybrid chain produced a series of single-particle cryo-EM structures that reveal features of interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during unfolding of ubiquitin. These results are consistent with cellular functions for SUMO and ubiquitin modifications and support a physical model wherein Ufd1/Npl4/Cdc48, SUMO, and ubiquitin conjugation pathways converge to promote clearance of proteins modified with SUMO and polyubiquitin.
History
DepositionJun 14, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27273.png

Downloads & links

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Map

FileDownload / File: emd_27273.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of substrate unbound class of particles. This class represents the portion of particles where Ufd1/Npl4/Cdc48 was not bound to the SUMO-ubiquitin(K48polyUb)-mEOS substrate. Composite map represents the composite map of overall and focused refinements under this deposition.
Projections & slices

Image control

Size
Brightness
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AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 384 pix.
= 408.576 Å		1.06 Å/pix.
x 384 pix.
= 408.576 Å		1.06 Å/pix.
x 384 pix.
= 408.576 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-32.560955 - 66.357730000000004
Average (Standard dev.)-0.02865957 (±1.0146987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 408.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focused refinement of the D1/D2 domains of Cdc48...

Fileemd_27273_additional_1.map
Annotationfocused refinement of the D1/D2 domains of Cdc48 of substrate unbound class of particles, post-processed
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement half map 1 of the D1/D2...

Fileemd_27273_additional_10.map
Annotationfocused refinement half map 1 of the D1/D2 domains of Cdc48 in substrate unbound class of particles
Projections & Slices
AxesZYX

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Histogram

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Additional map: focused refinement of cdc48 of substrate unbound class...

Fileemd_27273_additional_2.map
Annotationfocused refinement of cdc48 of substrate unbound class of particles, post-processed
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: overall refinement of substrate unbound class of particles,...

Fileemd_27273_additional_3.map
Annotationoverall refinement of substrate unbound class of particles, post-processed
Projections & Slices
AxesZYX

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Histogram

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Additional map: focused refinement of the central densities of Ufd1/Npl4...

Fileemd_27273_additional_4.map
Annotationfocused refinement of the central densities of Ufd1/Npl4 of substrate unbound class of particles, post-processed
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement half map 2 of the D1/D2...

Fileemd_27273_additional_5.map
Annotationfocused refinement half map 2 of the D1/D2 domains of Cdc48 of substrate unbound class of particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement half map 1 of Cdc48 of...

Fileemd_27273_additional_6.map
Annotationfocused refinement half map 1 of Cdc48 of substrate unbound class of particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: focused refinement half map 1 of the central...

Fileemd_27273_additional_7.map
Annotationfocused refinement half map 1 of the central Ufd1/Npl4 density of substrate unbound class of particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement half map 2 of Cdc48 of...

Fileemd_27273_additional_8.map
Annotationfocused refinement half map 2 of Cdc48 of substrate unbound class of particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focused refinement half map 2 of the central...

Fileemd_27273_additional_9.map
Annotationfocused refinement half map 2 of the central Ufd1/Npl4 density of substrate unbound class of particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: overall refinement half map 2 of substrate unbound class of particles

Fileemd_27273_half_map_1.map
Annotationoverall refinement half map 2 of substrate unbound class of particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: overall refinement half map 1 of substrate unbound class of particles

Fileemd_27273_half_map_2.map
Annotationoverall refinement half map 1 of substrate unbound class of particles
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in t...

EntireName: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP
Components
  • Complex: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP
    • Complex: Cdc48 hexamer
      • Protein or peptide: Cell division control protein 48
    • Complex: Ufd1/Npl4 tower
      • Protein or peptide: Nuclear protein localization protein 4
      • Protein or peptide: Ubiquitin fusion degradation protein 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in t...

SupramoleculeName: Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: This class represents the portion of particles where Ufd1/Npl4/Cdc48 was not bound to the SUMO-ubiquitin(K48polyUb)-mEOS substrate. Composite map represents the composite map of overall and ...Details: This class represents the portion of particles where Ufd1/Npl4/Cdc48 was not bound to the SUMO-ubiquitin(K48polyUb)-mEOS substrate. Composite map represents the composite map of overall and focused refinements under this deposition.

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Supramolecule #2: Cdc48 hexamer

SupramoleculeName: Cdc48 hexamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Ufd1/Npl4 tower

SupramoleculeName: Ufd1/Npl4 tower / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#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: 92.389195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMGEEHKP LLDASGVDPR EEDKTATAIL RRKKKDNMLL VDDAINDDNS VIAINSNTMD KLELFRGDTV LVKGKKRKDT VLIVLIDDE LEDGACRINR VVRNNLRIRL GDLVTIHPCP DIKYATRISV LPIADTIEGI TGNLFDVFLK PYFVEAYRPV R KGDHFVVR ...String:
GSHMGEEHKP LLDASGVDPR EEDKTATAIL RRKKKDNMLL VDDAINDDNS VIAINSNTMD KLELFRGDTV LVKGKKRKDT VLIVLIDDE LEDGACRINR VVRNNLRIRL GDLVTIHPCP DIKYATRISV LPIADTIEGI TGNLFDVFLK PYFVEAYRPV R KGDHFVVR GGMRQVEFKV VDVEPEEYAV VAQDTIIHWE GEPINREDEE NNMNEVGYDD IGGCRKQMAQ IREMVELPLR HP QLFKAIG IKPPRGVLMY GPPGTGKTLM ARAVANETGA FFFLINGPEV MSKMAGESES NLRKAFEEAE KNAPAIIFID EID SIAPKR DKTNGEVERR VVSQLLTLMD GMKARSNVVV IAATNRPNSI DPALRRFGRF DREVDIGIPD ATGRLEVLRI HTKN MKLAD DVDLEALAAE THGYVGADIA SLCSEAAMQQ IREKMDLIDL DEDEIDAEVL DSLGVTMDNF RFALGNSNPS ALRET VVES VNVTWDDVGG LDEIKEELKE TVEYPVLHPD QYTKFGLSPS KGVLFYGPPG TGKTLLAKAV ATEVSANFIS VKGPEL LSM WYGESESNIR DIFDKARAAA PTVVFLDELD SIAKARGGSL GDAGGASDRV VNQLLTEMDG MNAKKNVFVI GATNRPD QI DPAILRPGRL DQLIYVPLPD ENARLSILNA QLRKTPLEPG LELTAIAKAT QGFSGADLLY IVQRAAKYAI KDSIEAHR Q HEAEKEVKVE GEDVEMTDEG AKAEQEPEVD PVPYITKEHF AEAMKTAKRS VSDAELRRYE AYSQQMKASR GQFSNFNFN DAPLGTTATD NANSNNSAPS GAGAAFGSNA EEDDDLYS

UniProtKB: Cell division control protein 48

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Macromolecule #2: Nuclear protein localization protein 4

MacromoleculeName: Nuclear protein localization protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 66.144336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMLIRFRS KNGTHRVSCQ ENDLFGTVIE KLVGNLDPNA DVDTFTVCEK PGQGIHAVSE LADRTVMDLG LKHGDMLILN YSDKPANEK DGVNVEIGSV GIDSKGIRQH RYGPLRIKEL AVDEELEKED GLIPRQKSKL CKHGDRGMCE YCSPLPPWDK E YHEKNKIK ...String:
GSHMLIRFRS KNGTHRVSCQ ENDLFGTVIE KLVGNLDPNA DVDTFTVCEK PGQGIHAVSE LADRTVMDLG LKHGDMLILN YSDKPANEK DGVNVEIGSV GIDSKGIRQH RYGPLRIKEL AVDEELEKED GLIPRQKSKL CKHGDRGMCE YCSPLPPWDK E YHEKNKIK HISFHSYLKK LNENANKKEN GSSYISPLSE PDFRINKRCH NGHEPWPRGI CSKCQPSAIT LQQQEFRMVD HV EFQKSEI INEFIQAWRY TGMQRFGYMY GSYSKYDNTP LGIKAVVEAI YEPPQHDEQD GLTMDVEQVK NEMLQIDRQA QEM GLSRIG LIFTDLSDAG AGDGSVFCKR HKDSFFLSSL EVIMAARHQT RHPNVSKYSE QGFFSSKFVT CVISGNLEGE IDIS SYQVS TEAEALVTAD MISGSTFPSM AYINDTTDER YVPEIFYMKS NEYGITVKEN AKPAFPVDYL LVTLTHGFPN TDTET NSKF VSSTGFPWSN RQAMGQSQDY QELKKYLFNV ASSGDFNLLH EKISNFHLLL YINSLQILSP DEWKLLIESA VKNEWE ESL LKLVSSAGWQ TLVMILQESG

UniProtKB: Nuclear protein localization protein 4

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Macromolecule #3: Ubiquitin fusion degradation protein 1

MacromoleculeName: Ubiquitin fusion degradation protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 40.001449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMFSGFSSF GGGNGFVNMP QTFEEFFRCY PIAMMNDRIR KDDANFGGKI FLPPSALSKL SMLNIRYPML FKLTANETGR VTHGGVLEF IAEEGRVYLP QWMMETLGIQ PGSLLQISST DVPLGQFVKL EPQSVDFLDI SDPKAVLENV LRNFSTLTVD D VIEISYNG ...String:
GSMFSGFSSF GGGNGFVNMP QTFEEFFRCY PIAMMNDRIR KDDANFGGKI FLPPSALSKL SMLNIRYPML FKLTANETGR VTHGGVLEF IAEEGRVYLP QWMMETLGIQ PGSLLQISST DVPLGQFVKL EPQSVDFLDI SDPKAVLENV LRNFSTLTVD D VIEISYNG KTFKIKILEV KPESSSKSIC VIETDLVTDF APPVGYVEPD YKALKAQQDK EKKNSFGKGQ VLDPSVLGQG SM STRIDYA GIANSSRNKL SKFVGQGQNI SGKAPKAEPK QDIKDMKITF DGEPAKLDLP EGQLFFGFPM VLPKEDEESA AGS KSSEQN FQGQGISLRK SNKRKTKSDH DSSKSKAPKS PEVIEID

UniProtKB: Ubiquitin fusion degradation protein 1

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / 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 #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration2 mg/mL
BufferpH: 8
Details: 20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 8 s wait, 4 s blot before plunging.
DetailsUfd1/Npl4/Cdc48 was pre-incubated with SUMO-ubiquitin(K48polyUb)-mEOS and ATP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.577 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model from cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 346933
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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