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Yorodumi- EMDB-4166: Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet... -
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-Basic information
Entry | Database: EMDB / ID: EMD-4166 | |||||||||
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Title | Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 | |||||||||
Map data | TRIP13:p31-Substrate map | |||||||||
Sample |
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Function / homology | Function and homology information deactivation of mitotic spindle assembly checkpoint / metaphase/anaphase transition of cell cycle / mitotic spindle assembly checkpoint MAD1-MAD2 complex / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / meiotic recombination checkpoint signaling / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization ...deactivation of mitotic spindle assembly checkpoint / metaphase/anaphase transition of cell cycle / mitotic spindle assembly checkpoint MAD1-MAD2 complex / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / meiotic recombination checkpoint signaling / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / synaptonemal complex assembly / Phosphorylation of Emi1 / anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / regulation of exit from mitosis / positive regulation of synaptic plasticity / nuclear pore nuclear basket / anaphase-promoting complex binding / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / oocyte maturation / reciprocal meiotic recombination / female meiosis I / negative regulation of ubiquitin protein ligase activity / mitotic sister chromatid cohesion / oogenesis / mitotic spindle assembly checkpoint signaling / male meiosis I / spermatid development / regulation of mitotic cell cycle / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / Regulation of APC/C activators between G1/S and early anaphase / mitotic spindle assembly / negative regulation of mitotic cell cycle / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / APC/C:Cdc20 mediated degradation of Securin / male germ cell nucleus / SCF-beta-TrCP mediated degradation of Emi1 / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / transcription coregulator activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of protein catabolic process / spindle / mitotic spindle / kinetochore / spindle pole / Separation of Sister Chromatids / double-strand break repair / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / nervous system development / spermatogenesis / nuclear membrane / transcription by RNA polymerase II / cell differentiation / protein ubiquitination / Ub-specific processing proteases / cell division / centrosome / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / ATP hydrolysis activity / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Alfieri C / Chang L / Barford D | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2018 Title: Mechanism for remodelling of the cell cycle checkpoint protein MAD2 by the ATPase TRIP13. Authors: Claudio Alfieri / Leifu Chang / David Barford / Abstract: The maintenance of genome stability during mitosis is coordinated by the spindle assembly checkpoint (SAC) through its effector the mitotic checkpoint complex (MCC), an inhibitor of the anaphase- ...The maintenance of genome stability during mitosis is coordinated by the spindle assembly checkpoint (SAC) through its effector the mitotic checkpoint complex (MCC), an inhibitor of the anaphase-promoting complex (APC/C, also known as the cyclosome). Unattached kinetochores control MCC assembly by catalysing a change in the topology of the β-sheet of MAD2 (an MCC subunit), thereby generating the active closed MAD2 (C-MAD2) conformer. Disassembly of free MCC, which is required for SAC inactivation and chromosome segregation, is an ATP-dependent process driven by the AAA+ ATPase TRIP13. In combination with p31, an SAC antagonist, TRIP13 remodels C-MAD2 into inactive open MAD2 (O-MAD2). Here, we present a mechanism that explains how TRIP13-p31 disassembles the MCC. Cryo-electron microscopy structures of the TRIP13-p31-C-MAD2-CDC20 complex reveal that p31 recruits C-MAD2 to a defined site on the TRIP13 hexameric ring, positioning the N terminus of C-MAD2 (MAD2) to insert into the axial pore of TRIP13 and distorting the TRIP13 ring to initiate remodelling. Molecular modelling suggests that by gripping MAD2 within its axial pore, TRIP13 couples sequential ATP-driven translocation of its hexameric ring along MAD2 to push upwards on, and simultaneously rotate, the globular domains of the p31-C-MAD2 complex. This unwinds a region of the αA helix of C-MAD2 that is required to stabilize the C-MAD2 β-sheet, thus destabilizing C-MAD2 in favour of O-MAD2 and dissociating MAD2 from p31. Our study provides insights into how specific substrates are recruited to AAA+ ATPases through adaptor proteins and suggests a model of how translocation through the axial pore of AAA+ ATPases is coupled to protein remodelling. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4166.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-4166-v30.xml emd-4166.xml | 26 KB 26 KB | Display Display | EMDB header |
Images | emd_4166.png | 77.5 KB | ||
Others | emd_4166_additional_1.map.gz emd_4166_additional_2.map.gz emd_4166_additional_3.map.gz emd_4166_additional_4.map.gz emd_4166_additional_5.map.gz | 1.8 MB 2 MB 1.9 MB 1.9 MB 1.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4166 | HTTPS FTP |
-Related structure data
Related structure data | 6f0xMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4166.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TRIP13:p31-Substrate map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: TRIP13 apo map
File | emd_4166_additional_1.map | ||||||||||||
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Annotation | TRIP13_apo map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TRIP13:p31-Substrate basal state map
File | emd_4166_additional_2.map | ||||||||||||
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Annotation | TRIP13:p31-Substrate_basal_state map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TRIP13:p31-Substrate Activated state map
File | emd_4166_additional_3.map | ||||||||||||
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Annotation | TRIP13:p31-Substrate_Activated_state map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TRIP13:p31-Substrate All Particles map
File | emd_4166_additional_4.map | ||||||||||||
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Annotation | TRIP13:p31-Substrate_All_Particles map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TRIP13 A,B,C and D monomers map
File | emd_4166_additional_5.map | ||||||||||||
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Annotation | TRIP13_A,B,C and D monomers map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
Entire | Name: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 |
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Components |
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-Supramolecule #1: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
Supramolecule | Name: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 400 kDa/nm |
-Supramolecule #2: MAD2L1-binding protein, Pachytene checkpoint protein 2 homolog
Supramolecule | Name: MAD2L1-binding protein, Pachytene checkpoint protein 2 homolog type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: Cell division cycle protein 20 homolog, Mitotic spindle assembly ...
Supramolecule | Name: Cell division cycle protein 20 homolog, Mitotic spindle assembly checkpoint protein MAD2A type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Pachytene checkpoint protein 2 homolog
Macromolecule | Name: Pachytene checkpoint protein 2 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48.606664 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDEAVGDLKQ ALPCVAESPT VHVEVHQRGS STAKKEDINL SVRKLLNRHN IVFGDYTWTE FDEPFLTRNV QSVSIIDTEL KVKDSQPID LSACTVALHI FQLNEDGPSS ENLEEETENI IAANHWVLPA AEFHGLWDSL VYDVEVKSHL LDYVMTTLLF S DKNVNSNL ...String: MDEAVGDLKQ ALPCVAESPT VHVEVHQRGS STAKKEDINL SVRKLLNRHN IVFGDYTWTE FDEPFLTRNV QSVSIIDTEL KVKDSQPID LSACTVALHI FQLNEDGPSS ENLEEETENI IAANHWVLPA AEFHGLWDSL VYDVEVKSHL LDYVMTTLLF S DKNVNSNL ITWNRVVLLH GPPGTGKTSL CKALAQKLTI RLSSRYRYGQ LIEINSHSLF SKWFSESGKL VTKMFQKIQD LI DDKDALV FVLIDQVESL TAARNACRAG TEPSDAIRVV NAVLTQIDQI KRHSNVVILT TSNITEKIDV AFVDRADIKQ YIG PPSAAA IFKIYLSCLE ELMKCQIIYP RQQLLTLREL EMIGFIENNV SKLSLLLNDI SRKSEGLSGR VLRKLPFLAH ALYV QAPTV TIEGFLQALS LAVDKQFEER KKLAAYI |
-Macromolecule #2: MAD2L1-binding protein
Macromolecule | Name: MAD2L1-binding protein / 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: 31.086646 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAAPEAEVLS SAAVPDLEWY EKSEETHASQ IELLETSSTQ EPLNASEAFC PRDCMVPVVF PGPVSQEGCC QFTCELLKHI MYQRQQLPL PYEQLKHFYR KPSPQAEEML KKKPRATTEV SSRKCQQALA ELESVLSHLE DFFARTLVPR VLILLGGNAL S PKEFYELD ...String: MAAPEAEVLS SAAVPDLEWY EKSEETHASQ IELLETSSTQ EPLNASEAFC PRDCMVPVVF PGPVSQEGCC QFTCELLKHI MYQRQQLPL PYEQLKHFYR KPSPQAEEML KKKPRATTEV SSRKCQQALA ELESVLSHLE DFFARTLVPR VLILLGGNAL S PKEFYELD LSLLAPYSVD QSLSTAACLR RLFRAIFMAD AFSELQAPPL MGTVVMAQGH RNCGEDWFRP KLNYRVPSRG HK LTVTLSC GRPSIRTTAW EDYIWFQAPV TFKGFRE |
-Macromolecule #3: Cell division cycle protein 20 homolog
Macromolecule | Name: Cell division cycle protein 20 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.796508 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MAQFAFESDL HSLLQLDAPI PNAPPARWQR KAKEAAGPAP SPMRAANRSH SAGRTPGRTP GKSSSKVQTT PSKPGGDRYI PHRSAAQME VASFLLSKEN QPENSQTPTK KEHQKAWALN LNGFDVEEAK ILRLSGKPQN APEGYQNRLK VLYSQKATPG S SRKTCRYI ...String: MAQFAFESDL HSLLQLDAPI PNAPPARWQR KAKEAAGPAP SPMRAANRSH SAGRTPGRTP GKSSSKVQTT PSKPGGDRYI PHRSAAQME VASFLLSKEN QPENSQTPTK KEHQKAWALN LNGFDVEEAK ILRLSGKPQN APEGYQNRLK VLYSQKATPG S SRKTCRYI PSLPDRILDA PEIRNDYYLN LVDWSSGNVL AVALDNSVYL WSASSGDILQ LLQMEQPGEY ISSVAWIKEG NY LAVGTSS AEVQLWDVQQ QKRLRNMTSH SARVGSLSWN SYILSSGSRS GHIHHHDVRV AEHHVATLSG HSQEVCGLRW APD GRHLAS GGNDNLVNVW PSAPGEGGWV PLQTFTQHQG AVKAVAWCPW QSNVLATGGG TSDRHIRIWN VCSGACLSAV DAHS QVCSI LWSPHYKELI SGHGFAQNQL VIWKYPTMAK VAELKGHTSR VLSLTMSPDG ATVASAAADE TLRLWRCFEL DPARR RERE KASAAKSSLI HQGIR |
-Macromolecule #4: Mitotic spindle assembly checkpoint protein MAD2A
Macromolecule | Name: Mitotic spindle assembly checkpoint protein MAD2A / 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: 23.533883 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MALQLSREQG ITLRGSAEIV AEFFSFGINS ILYQRGIYPS ETFTRVQKYG LTLLVTTDLE LIKYLNNVVE QLKDWLYKCS VQKLVVVIS NIESGEVLER WQFDIECDKT AKDDSAPREK SQKAIQDEIR SVIRQITATV TFLPLLEVSC SFDLLIYTDK D LVVPEKWE ...String: MALQLSREQG ITLRGSAEIV AEFFSFGINS ILYQRGIYPS ETFTRVQKYG LTLLVTTDLE LIKYLNNVVE QLKDWLYKCS VQKLVVVIS NIESGEVLER WQFDIECDKT AKDDSAPREK SQKAIQDEIR SVIRQITATV TFLPLLEVSC SFDLLIYTDK D LVVPEKWE ESGPQFITNS EEVRLRSFTT TIHKVNSMVA YKIPVND |
-Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 5 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1-beta-1) / Number images used: 354157 |