+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15861 | ||||||||||||
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Title | p97-p37-SPI substrate complex | ||||||||||||
Map data | p97 complex with p37 adaptor and SPI substrate | ||||||||||||
Sample |
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Keywords | AAA+ ATPase / p97 / VCP / Cdc48 / unfoldase / protein phosphatase-1 / protein maturation / CHAPERONE | ||||||||||||
Function / homology | Function and homology information negative regulation of protein localization to centrosome / PTW/PP1 phosphatase complex / positive regulation of mitotic centrosome separation / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase regulator activity / protein phosphatase 1 binding / lamin binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process ...negative regulation of protein localization to centrosome / PTW/PP1 phosphatase complex / positive regulation of mitotic centrosome separation / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase regulator activity / protein phosphatase 1 binding / lamin binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / spindle pole centrosome / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / microtubule organizing center / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / protein-serine/threonine phosphatase / ubiquitin-specific protease binding / Triglyceride catabolism / Maturation of hRSV A proteins / ubiquitin-like protein ligase binding / entrainment of circadian clock by photoperiod / MHC class I protein binding / Golgi organization / phosphatase activity / establishment of mitotic spindle orientation / phosphoprotein phosphatase activity / cleavage furrow / blastocyst development / RHOH GTPase cycle / autophagosome maturation / autophagosome assembly / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / enzyme regulator activity / ERAD pathway / Mitotic Prometaphase / ATP metabolic process / EML4 and NUDC in mitotic spindle formation / endoplasmic reticulum unfolded protein response / Attachment and Entry / positive regulation of protein dephosphorylation / positive regulation of glial cell proliferation / Resolution of Sister Chromatid Cohesion / lipid droplet / viral genome replication / proteasome complex / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / RHO GTPases Activate Formins / Hh mutants are degraded by ERAD / macroautophagy / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / RAF activation / Translesion Synthesis by POLH / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / neuron differentiation / regulation of circadian rhythm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | ||||||||||||
Authors | van den Boom J / Marini G / Meyer H / Saibil H | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: EMBO J / Year: 2023 Title: Structural basis of ubiquitin-independent PP1 complex disassembly by p97. Authors: Johannes van den Boom / Guendalina Marini / Hemmo Meyer / Helen R Saibil / Abstract: The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is ...The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is unclear. Here, we present cryo-EM structures of p97 in the process of disassembling a protein phosphatase-1 (PP1) complex by extracting an inhibitory subunit from PP1. We show that PP1 and its partners SDS22 and inhibitor-3 (I3) are loaded tightly onto p97, surprisingly via a direct contact of SDS22 with the p97 N-domain. Loading is assisted by the p37 adapter that bridges two adjacent p97 N-domains underneath the substrate complex. A stretch of I3 is threaded into the central channel of the spiral-shaped p97 hexamer, while other elements of I3 are still attached to PP1. Thus, our data show how p97 arranges a protein complex between the p97 N-domain and central channel, suggesting a hold-and-extract mechanism for p97-mediated disassembly. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15861.map.gz | 116.7 MB | EMDB map data format | |
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Header (meta data) | emd-15861-v30.xml emd-15861.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15861_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_15861.png | 166.6 KB | ||
Others | emd_15861_half_map_1.map.gz emd_15861_half_map_2.map.gz | 98.7 MB 98.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15861 | HTTPS FTP |
-Validation report
Summary document | emd_15861_validation.pdf.gz | 901.7 KB | Display | EMDB validaton report |
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Full document | emd_15861_full_validation.pdf.gz | 901.2 KB | Display | |
Data in XML | emd_15861_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_15861_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15861 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15861 | HTTPS FTP |
-Related structure data
Related structure data | 8b5rMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15861.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | p97 complex with p37 adaptor and SPI substrate | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map 1
File | emd_15861_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_15861_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : p97 complex with p37 adaptor and SPI substrate
Entire | Name: p97 complex with p37 adaptor and SPI substrate |
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Components |
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-Supramolecule #1: p97 complex with p37 adaptor and SPI substrate
Supramolecule | Name: p97 complex with p37 adaptor and SPI substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4, #6, #5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transitional endoplasmic reticulum ATPase
Macromolecule | Name: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 90.265695 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MHHHHHHASG ADSKGDDLST AILKQKNRPN RLIVDEAINE DNSVVSLSQP KMDELQLFRG DTVLLKGKKR REAVCIVLSD DTCSDEKIR MNRVVRNNLR VRLGDVISIQ PCPDVKYGKR IHVLPIDDTV EGITGNLFEV YLKPYFLEAY RPIRKGDIFL V RGGMRAVE ...String: MHHHHHHASG ADSKGDDLST AILKQKNRPN RLIVDEAINE DNSVVSLSQP KMDELQLFRG DTVLLKGKKR REAVCIVLSD DTCSDEKIR MNRVVRNNLR VRLGDVISIQ PCPDVKYGKR IHVLPIDDTV EGITGNLFEV YLKPYFLEAY RPIRKGDIFL V RGGMRAVE FKVVETDPSP YCIVAPDTVI HCEGEPIKRE DEEESLNEVG YDDIGGCRKQ LAQIKEMVEL PLRHPALFKA IG VKPPRGI LLYGPPGTGK TLIARAVANE TGAFFFLING PEIMSKLAGE SESNLRKAFE EAEKNAPAII FIDELDAIAP KRE KTHGEV ERRIVSQLLT LMDGLKQRAH VIVMAATNRP NSIDPALRRF GRFDREVDIG IPDATGRLEI LQIHTKNMKL ADDV DLEQV ANETHGHVGA DLAALCSEAA LQAIRKKMDL IDLEDETIDA EVMNSLAVTM DDFRWALSQS NPSALRETVV EVPQV TWED IGGLEDVKRE LQELVQYPVE HPDKFLKFGM TPSKGVLFYG PPGCGKTLLA KAIANECQAN FISIKGPELL TMWFGE SEA NVREIFDKAR QAAPCVLFFD ELDSIAKARG GNIGDGGGAA DRVINQILTE MDGMSTKKNV FIIGATNRPD IIDPAIL RP GRLDQLIYIP LPDEKSRVAI LKANLRKSPV AKDVDLEFLA KMTNGFSGAD LTEICQRACK LAIRESIESE IRRERERQ T NPSAMEVEED DPVPEIRRDH FEEAMRFARR SVSDNDIRKY EMFAQTLQQS RGFGSFRFPS GNQGGAGPSQ GSGGGTGGS VYTEDNDDDL YG UniProtKB: Transitional endoplasmic reticulum ATPase |
-Macromolecule #2: I3 sequence being threaded through the p97 channel
Macromolecule | Name: I3 sequence being threaded through the p97 channel / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.890321 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-Macromolecule #3: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
Macromolecule | Name: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.030777 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MADLDKLNID SIIQRLLEVR GSKPGKNVQL QENEIRGLCL KSREIFLSQP ILLELEAPLK ICGDIHGQYY DLLRLFEYGG FPPESNYLF LGDYVDRGKQ SLETICLLLA YKIKYPENFF LLRGNHECAS INRIYGFYDE CKRRYNIKLW KTFTDCFNCL P IAAIVDEK ...String: MADLDKLNID SIIQRLLEVR GSKPGKNVQL QENEIRGLCL KSREIFLSQP ILLELEAPLK ICGDIHGQYY DLLRLFEYGG FPPESNYLF LGDYVDRGKQ SLETICLLLA YKIKYPENFF LLRGNHECAS INRIYGFYDE CKRRYNIKLW KTFTDCFNCL P IAAIVDEK IFCCHGGLSP DLQSMEQIRR IMRPTDVPDQ GLLCDLLWSD PDKDVLGWGE NDRGVSFTFG AEVVAKFLHK HD LDLICRA HQVVEDGYEF FAKRQLVTLF SAPNYCGEFD NAGAMMSVDE TLMCSFQILK PAEKKKPNAT RPVTPPRGMI TKQ AKK UniProtKB: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit |
-Macromolecule #4: Protein phosphatase 1 regulatory subunit 7
Macromolecule | Name: Protein phosphatase 1 regulatory subunit 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.616129 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAAERGAGQQ QSQEMMEVDR RVESEESGDE EGKKHSSGIV ADLSEQSLKD GEERGEEDPE EEHELPVDME TINLDRDAED VDLNHYRIG KIEGFEVLKK VKTLCLRQNL IKCIENLEEL QSLRELDLYD NQIKKIENLE ALTELEILDI SFNLLRNIEG V DKLTRLKK ...String: MAAERGAGQQ QSQEMMEVDR RVESEESGDE EGKKHSSGIV ADLSEQSLKD GEERGEEDPE EEHELPVDME TINLDRDAED VDLNHYRIG KIEGFEVLKK VKTLCLRQNL IKCIENLEEL QSLRELDLYD NQIKKIENLE ALTELEILDI SFNLLRNIEG V DKLTRLKK LFLVNNKISK IENLSNLHQL QMLELGSNRI RAIENIDTLT NLESLFLGKN KITKLQNLDA LTNLTVLSMQ SN RLTKIEG LQNLVNLREL YLSHNGIEVI EGLENNNKLT MLDIASNRIK KIENISHLTE LQEFWMNDNL LESWSDLDEL KGA RSLETV YLERNPLQKD PQYRRKVMLA LPSVRQIDAT FVRF UniProtKB: Protein phosphatase 1 regulatory subunit 7 |
-Macromolecule #5: UBX domain-containing protein 2B
Macromolecule | Name: UBX domain-containing protein 2B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.123238 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: FSGEGQKLGS L UniProtKB: UBX domain-containing protein 2B |
-Macromolecule #6: UBX domain-containing protein 2B
Macromolecule | Name: UBX domain-containing protein 2B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 9.75922 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: AVVLIDDSVP TTKIQIRLAD GSRLIQRFNS THRILDVRNF IVQSRPEFAA LDFILVTSFP NKELTDESLT LLEADILNTV LLQQLK UniProtKB: UBX domain-containing protein 2B |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8b5r: |