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- 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
TitleCryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
Map dataTRIP13:p31-Substrate map
Sample
  • Complex: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
    • Complex: MAD2L1-binding protein, Pachytene checkpoint protein 2 homolog
      • Protein or peptide: Pachytene checkpoint protein 2 homolog
      • Protein or peptide: MAD2L1-binding protein
    • Complex: Cell division cycle protein 20 homolog, Mitotic spindle assembly checkpoint protein MAD2ACell cycle
      • Protein or peptide: Cell division cycle protein 20 homologCell cycle
      • Protein or peptide: Mitotic spindle assembly checkpoint protein MAD2A
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
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
Mad1/Cdc20-bound-Mad2 binding protein / Mad1 and Cdc20-bound-Mad2 binding / Pachytene checkpoint protein 2-like / The WD repeat Cdc20/Fizzy family / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / Anaphase-promoting complex subunit 4, WD40 domain ...Mad1/Cdc20-bound-Mad2 binding protein / Mad1 and Cdc20-bound-Mad2 binding / Pachytene checkpoint protein 2-like / The WD repeat Cdc20/Fizzy family / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / ClpA/B family / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell division cycle protein 20 homolog / Mitotic spindle assembly checkpoint protein MAD2A / MAD2L1-binding protein / Pachytene checkpoint protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsAlfieri C / Chang L / Barford D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: 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
DepositionNov 20, 2017-
Header (metadata) releaseNov 29, 2017-
Map releaseMay 2, 2018-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0754
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0754
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f0x
  • Surface level: 0.0754
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4166.png

Downloads & links

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Map

FileDownload / File: emd_4166.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRIP13:p31-Substrate map
Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy AUTHOR: 0.0765 / Movie #1: 0.0754
Minimum - Maximum-0.18489556 - 0.3342573
Average (Standard dev.)0.0025145838 (±0.016992394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 200.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z200.200200.200200.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.1850.3340.003

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Supplemental data

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Additional map: TRIP13 apo map

Fileemd_4166_additional_1.map
AnnotationTRIP13_apo map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TRIP13:p31-Substrate basal state map

Fileemd_4166_additional_2.map
AnnotationTRIP13:p31-Substrate_basal_state map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TRIP13:p31-Substrate Activated state map

Fileemd_4166_additional_3.map
AnnotationTRIP13:p31-Substrate_Activated_state map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TRIP13:p31-Substrate All Particles map

Fileemd_4166_additional_4.map
AnnotationTRIP13:p31-Substrate_All_Particles map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TRIP13 A,B,C and D monomers map

Fileemd_4166_additional_5.map
AnnotationTRIP13_A,B,C and D monomers map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20

EntireName: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
Components
  • Complex: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
    • Complex: MAD2L1-binding protein, Pachytene checkpoint protein 2 homolog
      • Protein or peptide: Pachytene checkpoint protein 2 homolog
      • Protein or peptide: MAD2L1-binding protein
    • Complex: Cell division cycle protein 20 homolog, Mitotic spindle assembly checkpoint protein MAD2ACell cycle
      • Protein or peptide: Cell division cycle protein 20 homologCell cycle
      • Protein or peptide: Mitotic spindle assembly checkpoint protein MAD2A
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20

SupramoleculeName: TRIP13 hexamer in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 400 kDa/nm

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Supramolecule #2: MAD2L1-binding protein, Pachytene checkpoint protein 2 homolog

SupramoleculeName: MAD2L1-binding protein, Pachytene checkpoint protein 2 homolog
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Cell division cycle protein 20 homolog, Mitotic spindle assembly ...

SupramoleculeName: Cell division cycle protein 20 homolog, Mitotic spindle assembly checkpoint protein MAD2A
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Pachytene checkpoint protein 2 homolog

MacromoleculeName: Pachytene checkpoint protein 2 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.606664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: MAD2L1-binding protein

MacromoleculeName: MAD2L1-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.086646 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: Cell division cycle protein 20 homolog

MacromoleculeName: Cell division cycle protein 20 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.796508 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #4: Mitotic spindle assembly checkpoint protein MAD2A

MacromoleculeName: Mitotic spindle assembly checkpoint protein MAD2A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.533883 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 5 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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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

Concentration0.3 mg/mL
BufferpH: 7.5
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied 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

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