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- EMDB-32827: Cryo-EM structure of dodecamer P97 -

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Basic information

Entry
Database: EMDB / ID: EMD-32827
TitleCryo-EM structure of dodecamer P97
Map data
Sample
  • Complex: dodecamer complex of P97
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine
KeywordsAAA ATPase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cytoplasmic ubiquitin ligase complex / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination ...flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cytoplasmic ubiquitin ligase complex / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / NAD+ metabolic process / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / ubiquitin-specific protease binding / regulation of synapse organization / ciliary transition zone / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / intracellular membrane-bounded organelle / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / interstrand cross-link repair / ATP metabolic process / translesion synthesis / Attachment and Entry / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / negative regulation of protein localization to chromatin / proteasomal protein catabolic process / lipid droplet / ciliary tip / proteasome complex / viral genome replication / Josephin domain DUBs / macroautophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / establishment of protein localization / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry / ciliary basal body / protein ubiquitination / protein domain specific binding / DNA repair / DNA damage response / Neutrophil degranulation / ubiquitin protein ligase binding / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / ATP hydrolysis activity
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
Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu S / Wang T
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of dodecamer P97 at 2.99 Angstroms resolution
Authors: Liu S / Wang T
History
DepositionFeb 8, 2022-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32827.png

Downloads & links

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Map

FileDownload / File: emd_32827.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.331
Minimum - Maximum-2.3883224 - 3.8745933
Average (Standard dev.)0.0003018132 (±0.08258804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : dodecamer complex of P97

EntireName: dodecamer complex of P97
Components
  • Complex: dodecamer complex of P97
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine

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Supramolecule #1: dodecamer complex of P97

SupramoleculeName: dodecamer complex of P97 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.543727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVRN NLRVRLGDVI SIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR AVEFKVVETD PSPYCIVAPD T VIHCEGEP ...String:
NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVRN NLRVRLGDVI SIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR AVEFKVVETD PSPYCIVAPD T VIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RGILLYGPPG TGKTLIARAV AN ETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEVERRIVSQ LLTLMDGLKQ RAH VIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVANETHGH VGADLAALCS EAAL QAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIGGLEDV KRELQELVQY PVEHP DKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVREIFD KARQAAPCVL FFDELD SIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLDQLI YIPLPDEKSR VAILKAN LR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAMEV EEDDPVPEIR RDHFEEAM R FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPS

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #2: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.048098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVGYDDIGGC RKQLAQIKEM VELPLRHPAL FKAIGVKPPR GILLYGPPGT GKTLIARAVA NETGAFFFLI NGPEIMSKLA GESESNLRK AFEEAEKNAP AIIFIDELDA IAPKREKTHG EVERRIVSQL LTLMDGLKQR AHVIVMAATN RPNSIDPALR R FGRFDREV ...String:
EVGYDDIGGC RKQLAQIKEM VELPLRHPAL FKAIGVKPPR GILLYGPPGT GKTLIARAVA NETGAFFFLI NGPEIMSKLA GESESNLRK AFEEAEKNAP AIIFIDELDA IAPKREKTHG EVERRIVSQL LTLMDGLKQR AHVIVMAATN RPNSIDPALR R FGRFDREV DIGIPDATGR LEILQIHTKN MKLADDVDLE QVANETHGHV GADLAALCSE AALQAIRKKM DLIDLEDETI DA EVMNSLA VTMDDFRWAL SQSNPSALRE TVVEVPQVTW EDIGGLEDVK RELQELVQYP VEHPDKFLKF GMTPSKGVLF YGP PGCGKT LLAKAIANEC QANFISIKGP ELLTMWFGES EANVREIFDK ARQAAPCVLF FDELDSIAKA RGGNIGDGGG AADR VINQI LTEMDGMSTK KNVFIIGATN RPDIIDPAIL RPGRLDQLIY IPLPDEKSRV AILKANLRKS PVAKDVDLEF LAKMT NGFS GADLTEICQR ACKLAIRESI ESEIRRERQT QTNPSAMEVE EDDPVPEIRR DHFEEAMRFA RRSVSDNDIR KYEMFA QTL QQSRGFGSFR FPS

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #3: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.105184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EVGYDDIGGC RKQLAQIKEM VELPLRHPAL FKAIGVKPPR GILLYGPPGT GKTLIARAVA NETGAFFFLI NGPEIMSKLA GESESNLRK AFEEAEKNAP AIIFIDELDA IAPKREKTHG EVERRIVSQL LTLMDGLKQR AHVIVMAATN RPNSIDPALR R FGRFDREV ...String:
EVGYDDIGGC RKQLAQIKEM VELPLRHPAL FKAIGVKPPR GILLYGPPGT GKTLIARAVA NETGAFFFLI NGPEIMSKLA GESESNLRK AFEEAEKNAP AIIFIDELDA IAPKREKTHG EVERRIVSQL LTLMDGLKQR AHVIVMAATN RPNSIDPALR R FGRFDREV DIGIPDATGR LEILQIHTKN MKLADDVDLE QVANETHGHV GADLAALCSE AALQAIRKKM DLIDLEDETI DA EVMNSLA VTMDDFRWAL SQSNPSALRE TVVEVPQVTW EDIGGLEDVK RELQELVQYP VEHPDKFLKF GMTPSKGVLF YGP PGCGKT LLAKAIANEC QANFISIKGP ELLTMWFGES EANVREIFDK ARQAAPCVLF FDELDSIAKA RGGNIGDGGG AADR VINQI LTEMDGMSTK KNVFIIGATN RPDIIDPAIL RPGRLDQLIY IPLPDEKSRV AILKANLRKS PVAKDVDLEF LAKMT NGFS GADLTEICQR ACKLAIRESI ESEIRRERER QTNPSAMEVE EDDPVPEIRR DHFEEAMRFA RRSVSDNDIR KYEMFA QTL QQSRGFGSFR FPS

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / 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: 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)p...

MacromoleculeName: 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine
type: ligand / ID: 5 / Number of copies: 12 / Formula: Y6Y
Molecular weightTheoretical: 520.666 Da
Chemical component information

ChemComp-Y6Y:
3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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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 K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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