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- EMDB-13934: S.c. Condensin core in DNA- and ATP-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-13934
TitleS.c. Condensin core in DNA- and ATP-bound state
Map datadeepEMhancer processed cryoEM map S.c. Condensin in DNA- and ATP-bound state
Sample
  • Complex: ATP- and DNA- bound Sc Condensin core complex
    • DNA: DNA (35-MER)
    • DNA: DNA (35-MER)
    • Protein or peptide: Structural maintenance of chromosomes protein 4
    • Protein or peptide: Structural maintenance of chromosomes protein 2
    • Protein or peptide: Condensin complex subunit 2
    • Protein or peptide: Condensin complex subunit 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsSMC-motor protein / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy ...negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / DNA secondary structure binding / maintenance of rDNA / rDNA chromatin condensation / nucleophagy / synaptonemal complex assembly / condensed chromosome, centromeric region / mitotic chromosome condensation / chromosome condensation / silent mating-type cassette heterochromatin formation / minor groove of adenine-thymine-rich DNA binding / mitotic sister chromatid segregation / condensed chromosome / histone binding / double-stranded DNA binding / cell division / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Structural maintenance of chromosomes protein ...Condensin subunit 1 / Condensin complex subunit 1, N-terminal / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1, N-term / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette 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 1 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) / Saccharomyces cerevisiae CEN.PK113-7D (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLecomte L / Hassler M / Haering C / Eustermann S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)681365European Union
CitationJournal: Science / Year: 2022
Title: A hold-and-feed mechanism drives directional DNA loop extrusion by condensin.
Authors: Indra A Shaltiel / Sumanjit Datta / Léa Lecomte / Markus Hassler / Marc Kschonsak / Sol Bravo / Catherine Stober / Jenny Ormanns / Sebastian Eustermann / Christian H Haering /
Abstract: Structural maintenance of chromosomes (SMC) protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that ...Structural maintenance of chromosomes (SMC) protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that the active condensin complex entraps the bases of a DNA loop transiently in two separate chambers. Single-molecule imaging and cryo-electron microscopy suggest a putative power-stroke movement at the first chamber that feeds DNA into the SMC-kleisin ring upon adenosine triphosphate binding, whereas the second chamber holds on upstream of the same DNA double helix. Unlocking the strict separation of "motor" and "anchor" chambers turns condensin from a one-sided into a bidirectional DNA loop extruder. We conclude that the orientation of two topologically bound DNA segments during the SMC reaction cycle determines the directionality of DNA loop extrusion.
History
DepositionDec 3, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13934.png

Downloads & links

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Map

FileDownload / File: emd_13934.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer processed cryoEM map S.c. Condensin in DNA- and ATP-bound state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.015490817 - 2.0477026
Average (Standard dev.)0.0012713348 (±0.025289714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13934_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened cryoEM map S.c. Condensin in DNA- and ATP-bound state

Fileemd_13934_additional_1.map
Annotationunsharpened cryoEM map S.c. Condensin in DNA- and ATP-bound state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local resolution filtered and sharpened cryoEM map S.c....

Fileemd_13934_additional_2.map
Annotationlocal resolution filtered and sharpened cryoEM map S.c. Condensin in DNA- and ATP-bound state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM half map 1 S.c. Condensin in DNA- and ATP-bound state

Fileemd_13934_half_map_1.map
AnnotationcryoEM half map 1 S.c. Condensin in DNA- and ATP-bound state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM half map 1 S.c. Condensin in DNA- and ATP-bound state

Fileemd_13934_half_map_2.map
AnnotationcryoEM half map 1 S.c. Condensin in DNA- and ATP-bound state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATP- and DNA- bound Sc Condensin core complex

EntireName: ATP- and DNA- bound Sc Condensin core complex
Components
  • Complex: ATP- and DNA- bound Sc Condensin core complex
    • DNA: DNA (35-MER)
    • DNA: DNA (35-MER)
    • Protein or peptide: Structural maintenance of chromosomes protein 4
    • Protein or peptide: Structural maintenance of chromosomes protein 2
    • Protein or peptide: Condensin complex subunit 2
    • Protein or peptide: Condensin complex subunit 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ATP- and DNA- bound Sc Condensin core complex

SupramoleculeName: ATP- and DNA- bound Sc Condensin core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 645 kDa/nm

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Macromolecule #1: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 1
Details: 50-mer DNA ligand (sequence below) was modelled as poly-dA due to missing sequence register 5'-GTTGACAGTG TCGCAACCTG CACAGGCAAG CTGCTGAGTC TGGTGTAGAC-3'
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.615376 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)

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Macromolecule #2: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 2
Details: 50-mer DNA ligand (sequence below) was modelled as poly-dT due to missing sequence register. 5'-GTCTACACCAGACTCAGCAGCTTGCCTGTGCAGGTTGCGACACTGTCAAC-3'
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.164683 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

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Macromolecule #3: Structural maintenance of chromosomes protein 4

MacromoleculeName: Structural maintenance of chromosomes protein 4 / type: protein_or_peptide / ID: 3
Details: ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to ...Details: ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to delete the sequence corresponding to the coiled coil regions. This error needs to be corrected in communication with the pdb curator.,ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to delete the sequence corresponding to the coiled coil regions. This error needs to be corrected in communication with the pdb curator.,ATPase deficient Walker B motif mutant central coiled-coil region results in faulty sequence alignment as it was not build in the structure To circumvent this technical problem, we had to delete the sequence corresponding to the coiled coil regions. This error needs to be corrected in communication with the pdb curator.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae CEN.PK113-7D (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 167.716125 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString: MSDSPLSKRQ KRKAAQEPEL SLDQGDAEEE SQVENRVNLS ENTPEPDLPA LEASYSKSYT PRKLVLSSGE NRYAFSQPTN STTTSLHVP NLQPPKTSSR GRDHKSYSQS PPRSPGRSPT RRLEL(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK) ...String:
MSDSPLSKRQ KRKAAQEPEL SLDQGDAEEE SQVENRVNLS ENTPEPDLPA LEASYSKSYT PRKLVLSSGE NRYAFSQPTN STTTSLHVP NLQPPKTSSR GRDHKSYSQS PPRSPGRSPT RRLEL(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)YDSHQSSS KQQSRLFINE LVLENFKSYA GKQVVGP FH TSFSAVVGPN GSGKSNVIDS MLFVFGFRAN KMRQDRLSDL IHKSEAFPSL QSCSVAVHFQ YVIDESSGTS RIDEEKPG L IITRKAFKNN SSKYYINEKE SSYTEVTKLL KNEGIDLDHK RFLILQGEVE NIAQMKPKAE KESDDGLLEY LEDIIGTAN YKPLIEERMG QIENLNEVCL EKENRFEIVD REKNSLESGK ETALEFLEKE KQLTLLRSKL FQFKLLQSNS KLASTLEKIS SSNKDLEDE RMKFQESLKK VDEIKAQRKE IKDRISSCSS KEKTLVLERR ELEGTRVSLE ERTKNLVSKM EKAEKTLKST K HSISEAEN MLEELRGQQT EHETEIKDLT QLLEKERSIL DDIKLSLKDK TKDISAEIIR HEKELEPWDL QLQEKESQIQ LA ESELSLL EETQAKLKKN VETLEEKILA KKTHKQELQD LILDLKKKLN SLKDERSQGE KNFTSAHLKL KEMQKVLNAH RQR AMEARS SLSKAQNKSK VLTALSRLQK SGRINGFHGR LGDLGAIDDS FDIAISTACP RLDDVVVDTV ECAQHCIDYL RKNK LGYAR FILLDRLRQF NLQPISTPEN VPRLFDLVKP KNPKFSNAFY SVLRDTLVAQ NLKQANNVAY GKKRFRVVTV DGKLI DISG TMSGGGNHVA KGLMKLGTNQ SDKVDDYTPE EVDKIERELS ERENNFRVAS DTVHEMEEEL KKLRDHEPDL ESQISK AEM EADSLASELT LAEQQVKEAE MAYVKAVSDK AQLNVVMKNL ERLRGEYNDL QSETKTKKEK IKGLQDEIMK IGGIKLQ MQ NSKVESVCQK LDILVAKLKK VKSASKKSGG DVVKFQKLLQ NSERDVELSS NELKVIEEQL KHTKLALAEN DTNMTETL N LKVELKEQSE QLKEQMEDME ESINEFKSIE IEMKNKLEKL NSLLTYIKSE ITQQEKGLNE LSIRDVTHTL GMLDDNKMD SVKEDVKNNQ ELDQEYRSCE TQDESEIKDD ETSCDNYHPM NVDETSDEVS RGIPRLSEDE LRELDVELIE SKINELSYYV EETNVDIGV LEEYARRLAE FKRRKLDLNN AVQKRDEVKE QLGILKKKRF DEFMAGFNII SMTLKEMYQM ITMGGNAELE L VDSLDPFS EGVTFSVMPP KKSWRNITNL SGGEKTLSSL ALVFALHKYK PTPLYVMDQI DAALDFRNVS IVANYIKERT KN AQFIVIS LRNNMFELAQ QLVGVYKRDN RTKSTTIKNI DILNRTRIPG LINGATGWSH PQFEKAGGGS GGGSGGGSWS HPQ FEKGGG SGGGSGGGSW SHPQFEK

UniProtKB: Structural maintenance of chromosomes protein 4, Structural maintenance of chromosomes protein 4

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Macromolecule #4: Structural maintenance of chromosomes protein 2

MacromoleculeName: Structural maintenance of chromosomes protein 2 / type: protein_or_peptide / ID: 4 / Details: ATPase deficient Walker B motif mutant / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 134.124891 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 MYILDQVDAA LDL SHTQNI GHLIKTRFKG SQFIVVSLKE GMFANANRVF RTRFQDGTSV VSIM

UniProtKB: Structural maintenance of chromosomes protein 2

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Macromolecule #5: Condensin complex subunit 2

MacromoleculeName: Condensin complex subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 92.721219 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 KPAQKMSLFS 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 RPHHGGHHHH HHGGRIFYPY DVPDYAGYPY DVPDYAGSY PYDVPNYAAG H

UniProtKB: Condensin complex subunit 2

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Macromolecule #6: Condensin complex subunit 1

MacromoleculeName: Condensin complex subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 133.116766 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSGFSLSEYL TKFQTTDRES YPRLQDPSRE LNVIIDQLAV SPEQIDASPD SLEALIDLCH DFPHLTPKLQ TQLSYLISSS LSNLSKDIK ANLSSNVNFT EIGGLIPQWK RHLEEYGYLI QVLLTFLQDE LHKVSSQSTN LNRSAKNSKN DSANVELFKR D CNQMENLL ...String:
MSGFSLSEYL TKFQTTDRES YPRLQDPSRE LNVIIDQLAV SPEQIDASPD SLEALIDLCH DFPHLTPKLQ TQLSYLISSS LSNLSKDIK ANLSSNVNFT EIGGLIPQWK RHLEEYGYLI QVLLTFLQDE LHKVSSQSTN LNRSAKNSKN DSANVELFKR D CNQMENLL ESITKLLEIN LSKIFQTTPE KDLFIGLFTR PLFVLLEIEP VTKVSSLKMF IQRILAMCVK NHGQSSSIQS SL MTNLTYF LHLSVFNAEL LKLLNDEYNY PQLTEDILKE ISTRVFNAKD TTGPKAISNF LIKLSELSPG IMLRQMNLVI TLL NNSSIT LRCSVVEACG NIVAELAQDP QTMEHYKQQI AVLIELLEER FQDSNPYVRT KAIQGCSKIC DLSSKFNKSK AKFT SLAVR SLQDRSSLVR RNSVKLLSKL LLKHPFKAIH GSQLRLSEWE EYLKGSESQL NSTLKKVESQ ETLNDTIERS LIEEE VEQD EGQCRTELEG SFNKSAELSR IENEVENINA TNTSVLMKLK LMIVYYKDAI SFIKEIHKSI ELISNLLFSK NRNEVL ESM DFLVLADAFD IELSEFGIKK MLHLVWMKGT NDEGTSISVH LIECYKQLFL TAPDSCNMQE KAAHIAKNLI NLSIGAS IA DLASLEQLLG MMYEQKLIDQ HVINILWAIY NSASKASMQK EQNVNNRDSE KGFSKEQIHG SIIILGMLSL ADNEIALK G LESLLNIGLG AVGLKDLTLC RYSCLALERM VPKRSTIITK AINQELEDVA VKKLYAIIIN YTKDNEYYPM CEQALSALF TISSKPDILA TDLIREKTMM TFGKPEEEDS ILSLEQSSRV VSLSQLLFIV GQVAIKTLVY LEKCEAEFKK RKIEAETRNG KVKNQGADV TNTTQDNGGD KELEMIGGTN EDDFTDAIQF VKENELLFGE KSILGKFCPI VEEIVSNSSR FSDPMLQRTA T LCLEKLMC LSSKYCEKSL PLLITVMEKS PDPTIRSNAV LGLGDMAVCF NNLVDENTDY LYRRLHDENL MVQRTCLMTV TF LILAGQV KVKGQLGEMA KCLDNPDQGI SDMCRLFFTE LASKDNAIYN GFIDIFSNLS SDDLLGKESF KKIIKFLLTF IDK ERHQKQ LNEKLVGRLR KCETQKQWDD IAFVLNNLPY KNEDVTALLE QGFKVVSAKE

UniProtKB: Condensin complex subunit 1

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.645 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium Chloride
20.0 mMHepesHepes
1.0 mMDTTDithiothreitol
5.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil / Material: GOLD / Mesh: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6544 / Average exposure time: 8.0 sec. / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 91522
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 66205
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 95000 / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6yvu


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7qen:
S.c. Condensin core in DNA- and ATP-bound state

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