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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | p97-SPI substrate complex on subunit E | ||||||||||||
![]() | map of p97 with SPI substrate on subunit E | ||||||||||||
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![]() | AAA+ ATPase / p97 / VCP / Cdc48 / unfoldase / protein phosphatase-1 / protein maturation / CHAPERONE | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | ||||||||||||
![]() | Saibil H / van den Boom J / Marini G / Meyer H | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 116.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.6 KB | Display | ![]() |
Images | ![]() | 110.3 KB | ||
Others | ![]() ![]() | 98.5 MB 98.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 934.9 KB | Display | ![]() |
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Full document | ![]() | 934.5 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | map of p97 with SPI substrate on subunit E | ||||||||||||||||||||
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 2
File | emd_15846_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_15846_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : p97 SPI substrate complex on subunit E
Entire | Name: p97 SPI substrate complex on subunit E |
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Components |
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-Supramolecule #1: p97 SPI substrate complex on subunit E
Supramolecule | Name: p97 SPI substrate complex on subunit E / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: p97
Macromolecule | Name: p97 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHASG ADSKGDDLST AILKQKNRPN RLIVDEAINE DNSVVSLSQP KMDELQLFRG DTVLLKGKKR REAVCIVLSD DTCSDEKIRM NRVVRNNLRV RLGDVISIQP CPDVKYGKRI HVLPIDDTVE GITGNLFEVY LKPYFLEAYR PIRKGDIFLV RGGMRAVEFK ...String: MHHHHHHASG ADSKGDDLST AILKQKNRPN RLIVDEAINE DNSVVSLSQP KMDELQLFRG DTVLLKGKKR REAVCIVLSD DTCSDEKIRM NRVVRNNLRV RLGDVISIQP CPDVKYGKRI HVLPIDDTVE GITGNLFEVY LKPYFLEAYR PIRKGDIFLV RGGMRAVEFK VVETDPSPYC IVAPDTVIHC EGEPIKREDE EESLNEVGYD DIGGCRKQLA QIKEMVELPL RHPALFKAIG VKPPRGILLY GPPGTGKTLI ARAVANETGA FFFLINGPEI MSKLAGESES NLRKAFEEAE KNAPAIIFID ELDAIAPKRE KTHGEVERRI VSQLLTLMDG LKQRAHVIVM AATNRPNSID PALRRFGRFD REVDIGIPDA TGRLEILQIH TKNMKLADDV DLEQVANETH GHVGADLAAL CSEAALQAIR KKMDLIDLED ETIDAEVMNS LAVTMDDFRW ALSQSNPSAL RETVVEVPQV TWEDIGGLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVREIFD KARQAAPCVL FFDELDSIAK ARGGNIGDGG GAADRVINQI LTEMDGMSTK KNVFIIGATN RPDIIDPAIL RPGRLDQLIY IPLPDEKSRV AILKANLRKS PVAKDVDLEF LAKMTNGFSG ADLTEICQRA CKLAIRESIE SEIRRERERQ TNPSAMEVEE DDPVPEIRRD HFEEAMRFAR RSVSDNDIRK YEMFAQTLQQ SRGFGSFRFP SGNQGGAGPS QGSGGGTGGS VYTEDNDDDL YG |
-Macromolecule #2: SDS22
Macromolecule | Name: SDS22 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAAERGAGQQ QSQEMMEVDR RVESEESGDE EGKKHSSGIV ADLSEQSLKD GEERGEEDPE EEHELPVDME TINLDRDAED VDLNHYRIGK IEGFEVLKKV KTLCLRQNLI KCIENLEELQ SLRELDLYDN QIKKIENLEA LTELEILDIS FNLLRNIEGV DKLTRLKKLF ...String: MAAERGAGQQ QSQEMMEVDR RVESEESGDE EGKKHSSGIV ADLSEQSLKD GEERGEEDPE EEHELPVDME TINLDRDAED VDLNHYRIGK IEGFEVLKKV KTLCLRQNLI KCIENLEELQ SLRELDLYDN QIKKIENLEA LTELEILDIS FNLLRNIEGV DKLTRLKKLF LVNNKISKIE NLSNLHQLQM LELGSNRIRA IENIDTLTNL ESLFLGKNKI TKLQNLDALT NLTVLSMQSN RLTKIEGLQN LVNLRELYLS HNGIEVIEGL ENNNKLTMLD IASNRIKKIE NISHLTELQE FWMNDNLLES WSDLDELKGA RSLETVYLER NPLQKDPQYR RKVMLALPSV RQIDATFVRF |
-Macromolecule #3: PP1 gamma
Macromolecule | Name: PP1 gamma / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADLDKLNID SIIQRLLEVR GSKPGKNVQL QENEIRGLCL KSREIFLSQP ILLELEAPLK ICGDIHGQYY DLLRLFEYGG FPPESNYLFL GDYVDRGKQS LETICLLLAY KIKYPENFFL LRGNHECASI NRIYGFYDEC KRRYNIKLWK TFTDCFNCLP IAAIVDEKIF ...String: MADLDKLNID SIIQRLLEVR GSKPGKNVQL QENEIRGLCL KSREIFLSQP ILLELEAPLK ICGDIHGQYY DLLRLFEYGG FPPESNYLFL GDYVDRGKQS LETICLLLAY KIKYPENFFL LRGNHECASI NRIYGFYDEC KRRYNIKLWK TFTDCFNCLP IAAIVDEKIF CCHGGLSPDL QSMEQIRRIM RPTDVPDQGL LCDLLWSDPD KDVLGWGEND RGVSFTFGAE VVAKFLHKHD LDLICRAHQV VEDGYEFFAK RQLVTLFSAP NYCGEFDNAG AMMSVDETLM CSFQILKPAE KKKPNATRPV TPPRGMITKQ AKK |
-Macromolecule #4: I3
Macromolecule | Name: I3 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMA EAGAGLSETV TETTVTVTTE PENRSLTIKL RKRKPEKKVE WTSDTVDNEH MGRRSSKCCC IYEKPRAFGE SSTESDEEEE EGCGHTHCVR GHRKGRRRAT LGPTPTTPPQ PPDPSQPPPG PMQH |
-Macromolecule #5: p37 adaptor
Macromolecule | Name: p37 adaptor / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GPLGSMAEGG RAEPEEQERG SSRPRPPSAR DLQLALAELY EDEMKCKSSK PDRSTPATCR SPRTPPHRLY SGDHKYDGLH IVQPPTGKIV NELFKEAREH GAVPLNEATR SSREDKTKSF TGGGYRLGNS FYKRSEYIYG ENQLQDVQVL LKLWRNGFSL DDGELRPYSD ...String: GPLGSMAEGG RAEPEEQERG SSRPRPPSAR DLQLALAELY EDEMKCKSSK PDRSTPATCR SPRTPPHRLY SGDHKYDGLH IVQPPTGKIV NELFKEAREH GAVPLNEATR SSREDKTKSF TGGGYRLGNS FYKRSEYIYG ENQLQDVQVL LKLWRNGFSL DDGELRPYSD PTNAQFLESV KRGETPLELQ RLVHGAQVNL DMEDHQDQEY IKPRLRFKAF SGEGQKLGSL TPEIVSTPSS PEEEDKSILN AAVLIDDSMP TTKIQIRLAD GSRLVQRFNS THRILDVRDF IVRSRPEFAT TDFILVTSFP SKELTDETVT LQEADILNTV ILQQLK |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 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: ![]() |
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 |