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- EMDB-10944: Head segment of the S.cerevisiae condensin holocomplex in presenc... -

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Basic information

Entry
Database: EMDB / ID: EMD-10944
TitleHead segment of the S.cerevisiae condensin holocomplex in presence of ATP
Map data
Sample
  • Complex: condensin
    • Protein or peptide: Condensin complex subunit 2
    • Protein or peptide: Condensin complex subunit 3
    • Protein or peptide: Structural maintenance of chromosomes protein 2
    • Protein or peptide: Structural maintenance of chromosomes protein 4
KeywordsCondensin chromosome condensation SMC protein / CELL CYCLE
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation ...negative regulation of meiotic DNA double-strand break formation / Condensation of Prometaphase Chromosomes / meiotic chromosome condensation / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / condensed chromosome / double-stranded DNA binding / cell division / chromatin binding / chromatin / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Smc2, ATP-binding cassette domain / Nuclear condensin complex subunit 3, C-terminal domain / Condensin complex subunit 3 / Nuclear condensing complex subunits, C-term domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain ...Smc2, ATP-binding cassette domain / Nuclear condensin complex subunit 3, C-terminal domain / Condensin complex subunit 3 / Nuclear condensing complex subunits, C-term domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Condensin complex subunit 2 / Structural maintenance of chromosomes protein 2 / Condensin complex subunit 3 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsMerkel F / Haering CH
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2015-CoG 681365European Union
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.
Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol ...Authors: Byung-Gil Lee / Fabian Merkel / Matteo Allegretti / Markus Hassler / Christopher Cawood / Léa Lecomte / Francis J O'Reilly / Ludwig R Sinn / Pilar Gutierrez-Escribano / Marc Kschonsak / Sol Bravo / Takanori Nakane / Juri Rappsilber / Luis Aragon / Martin Beck / Jan Löwe / Christian H Haering /
Abstract: Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The ...Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.
History
DepositionApr 28, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yvd
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yvd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10944.png

Downloads & links

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Map

FileDownload / File: emd_10944.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.45 Å/pix.
x 100 pix.
= 244.8 Å		2.45 Å/pix.
x 100 pix.
= 244.8 Å		2.45 Å/pix.
x 100 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.448 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.11281216 - 0.20891753
Average (Standard dev.)0.0013217727 (±0.008698412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.4482.4482.448
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.1130.2090.001

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Supplemental data

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Mask #1

Fileemd_10944_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10944_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10944_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : condensin

EntireName: condensin
Components
  • Complex: condensin
    • Protein or peptide: Condensin complex subunit 2
    • Protein or peptide: Condensin complex subunit 3
    • Protein or peptide: Structural maintenance of chromosomes protein 2
    • Protein or peptide: Structural maintenance of chromosomes protein 4

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Supramolecule #1: condensin

SupramoleculeName: condensin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Engaged form in present of nucleotide
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 650 KDa

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Macromolecule #1: Condensin complex subunit 2

MacromoleculeName: Condensin complex subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 92.730164 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTTQLRYENN DDDERVEYNL FTNRSTMMAN FEEWIKMATD NKINSRNSWN FALIDYFYDL DVLKDGENNI NFQKASATLD GCIKIYSSR VDSVTTETGK LLSGLAQRKT NGASNGDDSN GGNGEGLGGD SDEANIEIDP LTGMPISNDP DVNNTRRRVY N RVLETTLV ...String:
MTTQLRYENN DDDERVEYNL FTNRSTMMAN FEEWIKMATD NKINSRNSWN FALIDYFYDL DVLKDGENNI NFQKASATLD GCIKIYSSR VDSVTTETGK LLSGLAQRKT NGASNGDDSN GGNGEGLGGD SDEANIEIDP LTGMPISNDP DVNNTRRRVY N RVLETTLV EFETIKMKEL DQELIIDPLF KKALVDFDEG GAKSLLLNTL NIDNTARVIF DASIKDTQNV GQGKLQRKEE EL IERDSLV DDENEPSQSL ISTRNDSTVN DSVISAPSME DEILSLGMDF IKFDQIAVCE ISGSIEQLRN VVEDINQAKD FIE NVNNRF DNFLTEEELQ AAVPDNAEDD SDGFDMGMQQ ELCYPDENHD NTSHDEQDDD NVNSTTGSIF EKDLMAYFDE NLNR NWRGR EHWKVRNFKK ANLVNKESDL LEETRTTIGD TTDKNTTDDK SMDTKKKHKQ KKVLEIDFFK TDDSFEDKVF ASKGR TKID MPIKNRKNDT HYLLPDDFHF STDRITRLFI KPGQKMSLFS HRKHTRGDVS SGLFEKSTVS ANHSNNDIPT IADEHF WAD NYERKEQEEK EKEQSKEVGD VVGGALDNPF EDDMDGVDFN QAFEGTDDNE EASVKLDLQD DEDHKFPIRE NKVTYSR VS KKVDVRRLKK NVWRSINNLI QEHDSRKNRE QSSNDSETHT EDESTKELKF SDIIQGISKM YSDDTLKDIS TSFCFICL L HLANEHGLQI THTENYNDLI VNYEDLATTQ AASLVGGGHH HHHHGGHHHH HHGGRIFYPY DVPDYAGYPY DVPDYAGSY PYDVPDYAAG H

UniProtKB: Condensin complex subunit 2

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Macromolecule #2: Condensin complex subunit 3

MacromoleculeName: Condensin complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 117.981 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MQDPDGIDIN TKIFNSVAEV FQKAQGSYAG HRKHIAVLKK IQSKAVEQGY EDAFNFWFDK LVTKILPLKK NEIIGDRIVK LVAAFIASL ERELILAKKQ NYKLTNDEEG IFSRFVDQFI RHVLRGVESP DKNVRFRVLQ LLAVIMDNIG EIDESLFNLL I LSLNKRIY ...String:
MQDPDGIDIN TKIFNSVAEV FQKAQGSYAG HRKHIAVLKK IQSKAVEQGY EDAFNFWFDK LVTKILPLKK NEIIGDRIVK LVAAFIASL ERELILAKKQ NYKLTNDEEG IFSRFVDQFI RHVLRGVESP DKNVRFRVLQ LLAVIMDNIG EIDESLFNLL I LSLNKRIY DREPTVRIQA VFCLTKFQDE EQTEHLTELS DNEENFEATR TLVASIQNDP SAEVRRAAML NLINDNNTRP YI LERARDV NIVNRRLVYS RILKSMGRKC FDDIEPHIFD QLIEWGLEDR ELSVRNACKR LIAHDWLNAL DGDLIELLEK LDV SRSSVC VKAIEALFQS RPDILSKIKF PESIWKDFTV EIAFLFRAIY LYCLDNNITE MLEENFPEAS KLSEHLNHYI LLRY HHNDI SNDSQSHFDY NTLEFIIEQL SIAAERYDYS DEVGRRSMLT VVRNMLALTT LSEPLIKIGI RVMKSLSINE KDFVT MAIE IINDIRDDDI EKQEQEEKIK SKKINRRNET SVDEEDENGT HNDEVNEDEE DDNISSFHSA VENLVQGNGN VSESDI INN LPPEKEASSA TIVLCLTRSS YMLELVNTPL TENILIASLM DTLITPAVRN TAPNIRELGV KNLGLCCLLD VKLAIDN MY ILGMCVSKGN ASLKYIALQV IVDIFSVHGN TVVDGEGKVD SISLHKIFYK VLKNNGLPEC QVIAAEGLCK LFLADVFT D DDLFETLVLS YFSPINSSNE ALVQAFAFCI PVYCFSHPAH QQRMSRTAAD ILLRLCVLWD DLQSSVIPEV DREAMLKPN IIFQQLLFWT DPRNLVNQTG STKKDTVQLT FLIDVLKIYA QIEKKEIKKM IITNINAIFL SSEQDYSTLK ELLEYSDDIA ENDNLDNVS KNALDKLRNN LNSLIEEINE RSETQTKDEN NTANDQYSSI LGNSFNKSSN DTIEHAADIT DGNNTELTKT T VNISAVDN TTEQSNSRKR TRSEAEQIDT SKNLENMSIQ DTSTVAKNVS FVLPDEKSDA MSIDEEDKDS ESFSEVC

UniProtKB: Condensin complex subunit 3

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Macromolecule #3: Structural maintenance of chromosomes protein 2

MacromoleculeName: Structural maintenance of chromosomes protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 134.125875 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKVEELIIDG FKSYATRTVI TDWDPQFNAI TGLNGSGKSN ILDAICFVLG IASMSTVRAS SLQDLIYKRG QAGVTKASVT IVFDNTDKS NSPIGFTNSP QISVTRQVVL GGTSKYLING HRAPQQSVLQ LFQSVQLNIN NPNFLIMQGK ITKVLNMKPS E ILSLIEEA ...String:
MKVEELIIDG FKSYATRTVI TDWDPQFNAI TGLNGSGKSN ILDAICFVLG IASMSTVRAS SLQDLIYKRG QAGVTKASVT IVFDNTDKS NSPIGFTNSP QISVTRQVVL GGTSKYLING HRAPQQSVLQ LFQSVQLNIN NPNFLIMQGK ITKVLNMKPS E ILSLIEEA AGTKMFEDRR EKAERTMSKK ETKLQENRTL LTEEIEPKLE KLRNEKRMFL EFQSTQTDLE KTERIVVSYE YY NIKHKHT SIRETLENGE TRMKMLNEFV KKTSEEIDSL NEDVEEIKLQ KEKELHKEGT ISKLENKENG LLNEISRLKT SLS IKVENL NDTTEKSKAL ESEIASSSAK LIEKKSAYAN TEKDYKMVQE QLSKQRDLYK RKEELVSTLT TGISSTGAAD GGYN AQLAK AKTELNEVSL AIKKSSMKME LLKKELLTIE PKLKEATKDN ELNVKHVKQC QETCDKLRAR LVEYGFDPSR IKDLK QRED KLKSHYYQTC KNSEYLKRRV TNLEFNYTKP YPNFEASFVH GVVGQLFQID NDNIRYATAL QTCAGGRLFN VVVQDS QTA TQLLERGRLR KRVTIIPLDK IYTRPISSQV LDLAKKIAPG KVELAINLIR FDESITKAME FIFGNSLICE DPETAKK IT FHPKIRARSI TLQGDVYDPE GTLSGGSRNT SESLLVDIQK YNQIQKQIET IQADLNHVTE ELQTQYATSQ KTKTIQSD L NLSLHKLDLA KRNLDANPSS QIIARNEEIL RDIGECENEI KTKQMSLKKC QEEVSTIEKD MKEYDSDKGS KLNELKKEL KLLAKELEEQ ESESERKYDL FQNLELETEQ LSSELDSNKT LLHNHLKSIE SLKLENSDLE GKIRGVEDDL VTVQTELNEE KKRLMDIDD ELNELETLIK KKQDEKKSSE LELQKLVHDL NKYKSNTNNM EKIIEDLRQK HEFLEDFDLV RNIVKQNEGI D LDTYRERS KQLNEKFQEL RKKVNPNIMN MIENVEKKEA ALKTMIKTIE KDKMKIQETI SKLNEYKRET LVKTWEKVTL DF GNIFADL LPNSFAKLVP CEGKDVTQGL EVKVKLGNIW KESLIELSGG QRSLIALSLI MALLQFRPAP MYILDEVDAA LDL SHTQNI GHLIKTRFKG SQFIVVSLKE GMFANANRVF RTRFQDGTSV VSIM

UniProtKB: Structural maintenance of chromosomes protein 2

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Macromolecule #4: Structural maintenance of chromosomes protein 4

MacromoleculeName: Structural maintenance of chromosomes protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 168.192625 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDSPLSKRQ KRKAAQEPEL SLDQGDAEEE SQVENRVNLS ENTPEPDLPA LEASYSKSYT PRKLVLSSGE NRYAFSQPTN STTTSLHVP NLQPPKTSSR GRDHKSYSQS PPRSPGRSPT RRLELLQLSP VKNSRVELQK IYDSHQSSSK QQSRLFINEL V LENFKSYA ...String:
MSDSPLSKRQ KRKAAQEPEL SLDQGDAEEE SQVENRVNLS ENTPEPDLPA LEASYSKSYT PRKLVLSSGE NRYAFSQPTN STTTSLHVP NLQPPKTSSR GRDHKSYSQS PPRSPGRSPT RRLELLQLSP VKNSRVELQK IYDSHQSSSK QQSRLFINEL V LENFKSYA GKQVVGPFHT SFSAVVGPNG SGKSNVIDSM LFVFGFRANK MRQDRLSDLI HKSEAFPSLQ SCSVAVHFQY VI DESSGTS RIDEEKPGLI ITRKAFKNNS SKYYINEKES SYTEVTKLLK NEGIDLDHKR FLILQGEVEN IAQMKPKAEK ESD DGLLEY LEDIIGTANY KPLIEERMGQ IENLNEVCLE KENRFEIVDR EKNSLESGKE TALEFLEKEK QLTLLRSKLF QFKL LQSNS KLASTLEKIS SSNKDLEDER MKFQESLKKV DEIKAQRKEI KDRISSCSSK EKTLVLERRE LEGTRVSLEE RTKNL VSKM EKAEKTLKST KHSISEAENM LEELRGQQTE HETEIKDLTQ LLEKERSILD DIKLSLKDKT KDISAEIIRH EKELEP WDL QLQEKESQIQ LAESELSLLE ETQAKLKKNV ETLEEKILAK KTHKQELQDL ILDLKKKLNS LKDERSQGEK NFTSAHL KL KEMQKVLNAH RQRAMEARSS LSKAQNKSKV LTALSRLQKS GRINGFHGRL GDLGAIDDSF DIAISTACPR LDDVVVDT V ECAQHCIDYL RKNKLGYARF ILLDRLRQFN LQPISTPENV PRLFDLVKPK NPKFSNAFYS VLRDTLVAQN LKQANNVAY GKKRFRVVTV DGKLIDISGT MSGGGNHVAK GLMKLGTNQS DKVDDYTPEE VDKIERELSE RENNFRVASD TVHEMEEELK KLRDHEPDL ESQISKAEME ADSLASELTL AEQQVKEAEM AYVKAVSDKA QLNVVMKNLE RLRGEYNDLQ SETKTKKEKI K GLQDEIMK IGGIKLQMQN SKVESVCQKL DILVAKLKKV KSASKKSGGD VVKFQKLLQN SERDVELSSN ELKVIEEQLK HT KLALAEN DTNMTETLNL KVELKEQSEQ LKEQMEDMEE SINEFKSIEI EMKNKLEKLN SLLTYIKSEI TQQEKGLNEL SIR DVTHTL GMLDDNKMDS VKEDVKNNQE LDQEYRSCET QDESEIKDDE TSCDNYHPMN VDETSDEVSR GIPRLSEDEL RELD VELIE SKINELSYYV EETNVDIGVL EEYARRLAEF KRRKLDLNNA VQKRDEVKEQ LGILKKKRFD EFMAGFNIIS MTLKE MYQM ITMGGNAELE LVDSLDPFSE GVTFSVMPPK KSWRNITNLS GGEKTLSSLA LVFALHKYKP TPLYVMDEID AALDFR NVS IVANYIKERT KNAQFIVISL RNNMFELAQQ LVGVYKRDNR TKSTTIKNID ILNRTRIPGL INGATGWSHP QFEKAGG GS GGGSGGGSWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Structural maintenance of chromosomes protein 4

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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: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87744
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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