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- EMDB-15861: p97-p37-SPI substrate complex -

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Basic information

Entry
Database: EMDB / ID: EMD-15861
Titlep97-p37-SPI substrate complex
Map datap97 complex with p37 adaptor and SPI substrate
Sample
  • Complex: p97 complex with p37 adaptor and SPI substrate
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: I3 sequence being threaded through the p97 channel
    • Protein or peptide: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 7
    • Protein or peptide: UBX domain-containing protein 2B
    • Protein or peptide: UBX domain-containing protein 2B
KeywordsAAA+ ATPase / p97 / VCP / Cdc48 / unfoldase / protein phosphatase-1 / protein maturation / CHAPERONE
Function / homology
Function and homology information


negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase 1 binding / lamin binding / protein phosphatase regulator activity / spindle pole centrosome / flavin adenine dinucleotide catabolic process ...negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / PTW/PP1 phosphatase complex / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase 1 binding / lamin binding / protein phosphatase regulator activity / spindle pole centrosome / flavin adenine dinucleotide catabolic process / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cytoplasmic ubiquitin ligase complex / 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 / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / protein dephosphorylation / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / NAD+ metabolic process / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / glycogen metabolic process / stress granule disassembly / protein-serine/threonine phosphatase / Triglyceride catabolism / ATPase complex / entrainment of circadian clock by photoperiod / ubiquitin-specific protease binding / establishment of mitotic spindle orientation / Golgi organization / regulation of synapse organization / protein serine/threonine phosphatase activity / ciliary transition zone / cleavage furrow / phosphatase activity / Maturation of hRSV A proteins / microtubule organizing center / mitotic sister chromatid segregation / positive regulation of ATP biosynthetic process / intracellular membrane-bounded organelle / ubiquitin-like protein ligase binding / RHOH GTPase cycle / MHC class I protein binding / positive regulation of glial cell proliferation / autophagosome maturation / blastocyst development / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / polyubiquitin modification-dependent protein binding / autophagosome assembly / interstrand cross-link repair / ATP metabolic process / translesion synthesis / enzyme regulator activity / Attachment and Entry / Protein methylation / negative regulation of protein localization to chromatin / endoplasmic reticulum unfolded protein response / phosphoprotein phosphatase activity / ERAD pathway / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / proteasomal protein catabolic process / lipid droplet / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / ciliary tip / proteasome complex / viral genome replication / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / macroautophagy / circadian regulation of gene expression / negative regulation of smoothened signaling pathway / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / establishment of protein localization / positive regulation of protein-containing complex assembly / RAF activation / Hh mutants are degraded by ERAD / RHO GTPases Activate Formins / Hedgehog ligand biogenesis
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. ...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. / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / 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 / Leucine-rich repeat, SDS22-like subfamily / CDC48 domain 2-like superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Aspartate decarboxylase-like domain superfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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
Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Transitional endoplasmic reticulum ATPase / UBX domain-containing protein 2B / Protein phosphatase 1 regulatory subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
Authorsvan den Boom J / Marini G / Meyer H / Saibil H
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust106249/Z/14/Z United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: 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
DepositionSep 24, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15861.png

Downloads & links

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Map

FileDownload / File: emd_15861.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationp97 complex with p37 adaptor and SPI substrate
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0026
Minimum - Maximum-0.011671251 - 0.022583729
Average (Standard dev.)0.0000136676545 (±0.0010406744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_15861_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_15861_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : p97 complex with p37 adaptor and SPI substrate

EntireName: p97 complex with p37 adaptor and SPI substrate
Components
  • Complex: p97 complex with p37 adaptor and SPI substrate
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: I3 sequence being threaded through the p97 channel
    • Protein or peptide: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
    • Protein or peptide: Protein phosphatase 1 regulatory subunit 7
    • Protein or peptide: UBX domain-containing protein 2B
    • Protein or peptide: UBX domain-containing protein 2B

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Supramolecule #1: p97 complex with p37 adaptor and SPI substrate

SupramoleculeName: p97 complex with p37 adaptor and SPI substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4, #6, #5
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: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.265695 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #2: I3 sequence being threaded through the p97 channel

MacromoleculeName: I3 sequence being threaded through the p97 channel / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.890321 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.030777 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #4: Protein phosphatase 1 regulatory subunit 7

MacromoleculeName: Protein phosphatase 1 regulatory subunit 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.616129 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #5: UBX domain-containing protein 2B

MacromoleculeName: UBX domain-containing protein 2B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.123238 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
FSGEGQKLGS L

UniProtKB: UBX domain-containing protein 2B

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Macromolecule #6: UBX domain-containing protein 2B

MacromoleculeName: UBX domain-containing protein 2B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.75922 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
AVVLIDDSVP TTKIQIRLAD GSRLIQRFNS THRILDVRNF IVQSRPEFAA LDFILVTSFP NKELTDESLT LLEADILNTV LLQQLK

UniProtKB: UBX domain-containing protein 2B

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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: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191477
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8b5r:
p97-p37-SPI substrate complex

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