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

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Basic information

Entry
Database: EMDB / ID: EMD-32827

*YMImages and movies for this entry are currently under preparation

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
Function / homology
Function and homology information


flavin adenine dinucleotide catabolic process / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding ...flavin adenine dinucleotide catabolic process / positive regulation of Lys63-specific deubiquitinase activity / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of oxidative phosphorylation / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / ERAD pathway / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / ER-associated misfolded protein catabolic process / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of mitochondrial membrane potential / ATPase complex / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / ubiquitin-specific protease binding / negative regulation of smoothened signaling pathway / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / Attachment and Entry / endoplasmic reticulum to Golgi vesicle-mediated transport / Protein methylation / HSF1 activation / MHC class I protein binding / ATP metabolic process / translesion synthesis / endoplasmic reticulum unfolded protein response / interstrand cross-link repair / lipid droplet / viral genome replication / ubiquitin-dependent ERAD pathway / Josephin domain DUBs / proteasome complex / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / proteasomal protein catabolic process / ADP binding / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / positive regulation of protein-containing complex assembly / Translesion Synthesis by POLH / ABC-family proteins mediated transport / positive regulation of protein catabolic process / double-strand break repair / establishment of protein localization / Aggrephagy / cytoplasmic stress granule / autophagy / azurophil granule lumen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / site of double-strand break / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to heat / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry / secretory granule lumen / protein phosphatase binding / protein ubiquitination / ficolin-1-rich granule lumen / regulation of apoptotic process / lipid binding / glutamatergic synapse / DNA repair / intracellular membrane-bounded organelle / protein domain specific binding / cellular response to DNA damage stimulus / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / ATP hydrolysis activity / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / 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 / Cell division protein 48 (CDC48) domain 2 / Cell division protein 48 (CDC48), domain 2 / CDC48, domain 2 / CDC48 domain 2-like superfamily / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation 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 / Cell division protein 48 (CDC48) domain 2 / Cell division protein 48 (CDC48), domain 2 / CDC48, domain 2 / CDC48 domain 2-like superfamily / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / Aspartate decarboxylase-like domain superfamily / AAA+ lid domain / AAA ATPase, AAA+ lid domain / AAA-protein family signature. / ATPase, AAA-type, conserved site / 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-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

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
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 / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia (bacteria)

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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

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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

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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

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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 / Adenosine diphosphate

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157000

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