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- EMDB-10930: Cohesin complex with loader gripping DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-10930
TitleCohesin complex with loader gripping DNA
Map data
Sample
  • Complex: Cohesin complex with loader gripping DNA
    • Complex: Cohesin subunit rad21, Structural maintenance of chromosomes protein 1 and 3
      • Protein or peptide: Cohesin subunit rad21
      • Protein or peptide: Structural maintenance of chromosomes protein 1
      • Protein or peptide: Structural maintenance of chromosomes protein 3
    • Complex: DNA (32-MER)
      • DNA: DNA (32-MER)
      • DNA: DNA (32-MER)
    • Complex: Sister chromatid cohesion protein mis4
      • Protein or peptide: Sister chromatid cohesion protein mis4
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


pericentric heterochromatin => GO:0005721 / meiotic cohesin complex => GO:0030893 / mitotic cohesin dsDNA (leading strand) loading / positive regulation of mitotic cohesin loading / Cohesin Loading onto Chromatin / Resolution of Sister Chromatid Cohesion / mitotic cohesin ssDNA (lagging strand) loading / maintenance of mitotic sister chromatid cohesion, centromeric / mitotic cohesin complex => GO:0030892 / : ...pericentric heterochromatin => GO:0005721 / meiotic cohesin complex => GO:0030893 / mitotic cohesin dsDNA (leading strand) loading / positive regulation of mitotic cohesin loading / Cohesin Loading onto Chromatin / Resolution of Sister Chromatid Cohesion / mitotic cohesin ssDNA (lagging strand) loading / maintenance of mitotic sister chromatid cohesion, centromeric / mitotic cohesin complex => GO:0030892 / : / SUMOylation of DNA damage response and repair proteins / nucleus leading edge / SMC loading complex / mitotic telomere tethering at nuclear periphery / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / cohesin loader activity / heterochromatin island / maintenance of mitotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / establishment of protein localization to chromatin / chromosome, subtelomeric region / rDNA heterochromatin / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / condensed chromosome, centromeric region / sister chromatid cohesion / mitotic sister chromatid cohesion / nuclear chromosome / mitotic sister chromatid segregation / enzyme regulator activity / pericentric heterochromatin / double-strand break repair / single-stranded DNA binding / chromosome / double-stranded DNA binding / cell division / DNA damage response / chromatin binding / chromatin / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic ...Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / 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-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 3 / Structural maintenance of chromosomes protein 1 / Cohesin subunit rad21 / Sister chromatid cohesion protein mis4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) / Synthetic construct (others) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsHigashi TL / Eickhoff P / Sousa JS / Costa A / Uhlmann F
Funding support2 items
OrganizationGrant numberCountry
European Research Council (ERC)
The Francis Crick Institute
CitationJournal: Mol Cell / Year: 2020
Title: A Structure-Based Mechanism for DNA Entry into the Cohesin Ring.
Authors: Torahiko L Higashi / Patrik Eickhoff / Joana S Sousa / Julia Locke / Andrea Nans / Helen R Flynn / Ambrosius P Snijders / George Papageorgiou / Nicola O'Reilly / Zhuo A Chen / Francis J ...Authors: Torahiko L Higashi / Patrik Eickhoff / Joana S Sousa / Julia Locke / Andrea Nans / Helen R Flynn / Ambrosius P Snijders / George Papageorgiou / Nicola O'Reilly / Zhuo A Chen / Francis J O'Reilly / Juri Rappsilber / Alessandro Costa / Frank Uhlmann /
Abstract: Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here we combine biochemical approaches and ...Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here we combine biochemical approaches and cryoelectron microscopy (cryo-EM) to visualize a cohesin loading intermediate in which DNA is locked between two gates that lead into the cohesin ring. Building on this structural framework, we design experiments to establish the order of events during cohesin loading. In an initial step, DNA traverses an N-terminal kleisin gate that is first opened upon ATP binding and then closed as the cohesin loader locks the DNA against the ATPase gate. ATP hydrolysis will lead to ATPase gate opening to complete DNA entry. Whether DNA loading is successful or results in loop extrusion might be dictated by a conserved kleisin N-terminal tail that guides the DNA through the kleisin gate. Our results establish the molecular basis for cohesin loading onto DNA.
History
DepositionApr 27, 2020-
Header (metadata) releaseAug 19, 2020-
Map releaseAug 19, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
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  • Surface view with fitted model
  • Atomic models: PDB-6yuf
  • Surface level: 0.5
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10930.png

Downloads & links

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Map

FileDownload / File: emd_10930.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.6519822 - 4.0692687
Average (Standard dev.)0.0034919416 (±0.06525339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z392.400392.400392.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.6524.0690.003

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Supplemental data

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Additional map: density modified map produced with Phenix resolve cryo-EM tool

Fileemd_10930_additional.map
Annotationdensity modified map produced with Phenix resolve cryo-EM tool
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10930_half_map_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_10930_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cohesin complex with loader gripping DNA

EntireName: Cohesin complex with loader gripping DNA
Components
  • Complex: Cohesin complex with loader gripping DNA
    • Complex: Cohesin subunit rad21, Structural maintenance of chromosomes protein 1 and 3
      • Protein or peptide: Cohesin subunit rad21
      • Protein or peptide: Structural maintenance of chromosomes protein 1
      • Protein or peptide: Structural maintenance of chromosomes protein 3
    • Complex: DNA (32-MER)
      • DNA: DNA (32-MER)
      • DNA: DNA (32-MER)
    • Complex: Sister chromatid cohesion protein mis4
      • Protein or peptide: Sister chromatid cohesion protein mis4
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cohesin complex with loader gripping DNA

SupramoleculeName: Cohesin complex with loader gripping DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: Cohesin subunit rad21, Structural maintenance of chromosomes prot...

SupramoleculeName: Cohesin subunit rad21, Structural maintenance of chromosomes protein 1 and 3
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: DNA (32-MER)

SupramoleculeName: DNA (32-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Synthetic construct (others)
Recombinant expressionOrganism: Synthetic construct (others)

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Supramolecule #4: Sister chromatid cohesion protein mis4

SupramoleculeName: Sister chromatid cohesion protein mis4 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)

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Macromolecule #1: Cohesin subunit rad21

MacromoleculeName: Cohesin subunit rad21 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 67.913711 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFYSEAILSK KGPLAKVWLA AHWEKKLSKV QTLHTSIEQS VHAIVTEETA PMALRLSGQL MLGVVRIYSR KARYLLEDCT EALMRLKMS FQPGQVDMIE PATALQSLKG KDAVTQSANL TLPETITEFD LLVPDSTFDF QWSQLLRTPS RSSNTLELHS L PISSSPSF ...String:
MFYSEAILSK KGPLAKVWLA AHWEKKLSKV QTLHTSIEQS VHAIVTEETA PMALRLSGQL MLGVVRIYSR KARYLLEDCT EALMRLKMS FQPGQVDMIE PATALQSLKG KDAVTQSANL TLPETITEFD LLVPDSTFDF QWSQLLRTPS RSSNTLELHS L PISSSPSF PSSQLSIEAG RNAQVESGFS LGESFAHVGN DMQFHLPISN SGAATPRSVH SDNQSQISIE VGRDAPAAAA TD LSGIIGP QMTKSPASSV THFSTPSMLP IGGTSLDDEL LAPVDDLNLD LGLDDLLGDE QGANAPAIEA DEQAETSSIH LPS DIMEDD SSRPAAAGVE EGQVVESATA PQQEKINPQK TVRRQRAIID PVTELSSKQM KKQLADTSSI TSPLCLNTSS IVFN ATVNF TRNGKFNTSI FSSNLNPKVN ELLQADFKQA ILRKRKNESP EEVEPAKHQR TDTSTENQET AEVLDPEEIA AAELA NITE AAIATLPQET VVQPEGEAPE LGSPMGFPVT ALESADDSLF DAPPVMLDEA DLLGSERLDS SVSEALPSSQ TAKDSL RNK WDPYTEGEKV SFQTLSAGCN REEAVQLFFD VLVLATKDVI SVKQDVAIQN EITLTAKRGM LLSSL

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Macromolecule #2: Sister chromatid cohesion protein mis4

MacromoleculeName: Sister chromatid cohesion protein mis4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 180.92475 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MLFEMTPETF KKVNSSNRII KGLQYTPLAS SIPLENGLQN VLYPSSKFQN EPLQLNSEES SIMQRYVDML NPGATFVNDS ETFNFYKNA LSAMITEPAM PAMRVNASPV LDQKVCNSDS LSELNDFTKS LIQPSMLMCE PKEKPDASSI NTNRSSSDNG F LTPSSSPR ...String:
MLFEMTPETF KKVNSSNRII KGLQYTPLAS SIPLENGLQN VLYPSSKFQN EPLQLNSEES SIMQRYVDML NPGATFVNDS ETFNFYKNA LSAMITEPAM PAMRVNASPV LDQKVCNSDS LSELNDFTKS LIQPSMLMCE PKEKPDASSI NTNRSSSDNG F LTPSSSPR SPSCSRVFNA VQLCSPKKSK DDITTPKKRL MEDTYSPRES PSKIQRLQDV LLKQLQDTRL LISQVIEAEN SE DFSSNSL FIKREDDDGK HISSHAIEKL YMALTKLSRL GACDKLLEEG SIILVKQILE KELKELPVAC YSIINLHDSL TQF PNLDFI LKTTALVLFI IFLVPSFKKL QNEESILHLL NILHSIFEYT VPEAIDNIVQ SKTSDARTSE IQHLSVLLQK VANV LNILS KVAHEIPLSE AVVIRIVYLF PKVSTLDNSF KTKLPNCNSS SFDFLKAPLF QTLQYLFRLY PYQRDFIIEE SLTNF SHLP TARSVSRTYR LSNGKSIQYY STLFVRLIQS CSIQNLFDSE IVQSESKSTE ALHSGNLTEH LKTVESILSK SRHEEY RIA NHIVAYLLSR SLKQNKTESD NSFAILTKIL LEDLLNMLSL PEWCGTETII RQFAMNLVMT VTNDKQAVSS KNAALDL IS LIVNKVLALF DLSLFEKHNI PAPTNFNDII SFIPSITRLN ELSQVSFNHF YFLCKGDISL ENILPYNYNK WFSFLLQL R KVCNDSEALK IIDNCIDKNM QKSQEGFQGP SPFKADENDE DIFIISLYHS SLFLNLKFFV SLIIGFLDSP QASLRTKCL RIINQMKTIP SILRTHPEVL AQIISKSNDQ SAIVRDTVLD LLGTYIMAYR ETIPQIYGCI ISGISDPSTI VRKRAIKQLC EVYEATEDL NIRVDIASKL LTRSNDEEET ISELSLEVLE KLWFSPASNE LDCQKGYEQL TFLEKQKLRV QYFPILKLCA E PSTERHVL LVTSLKTMLT SKEEINLSTL HTQIRLLLSC LFNQLIEVVT EDQVDESTKG ILYEIMSTLF VFSRAFPFLF DL SYLHLLK PYLRSASTIE EQRFLYYVVA IFRQVLPFQK EISESFLRSL ESVLLQRLTK AGTATLMEIV PCLCSLFTRL NDY ERLKKI VVSCLKSLEE ARHSENNFQK MVRLIDLIGL FSRYGDLNRI NDDWKHSLDF ISPECDDAYV ILLGYFQKLL KDAK GQLRI HIIDNMSRIC LRETSLFISP LMLSTLDMII AENNVNEVSV LFKSFLELLA ADEDLIFEAD QKLSLKGKQN VQSNK SVDR DMLKGTKDKQ WIEGVSASLM QHFLPCILDS CFSKNLRYSM LGIEILKCII HQGLVNPRMC FSTIIALESN AIKETR EVA ILLHTELHRR HESLIDGLYA QSADLIFSLQ KTEEYQTFKL GEFSPFQSAY TIVSADKSSK SRKKLIMQIL KPLKLDG ID LPSFTEEKVS FVSFCCVCLA GIPYVSIEEP LMIISTVDSV LATIGPTITG WMKKLDHERF KILAGINLCN LIYLKRYI K YAFSISDSSR PIREKKPLTL LNRGYVDLIT SDAKPDIVSK LVIKLFEEEN ILSGEDQVEG EQLTVV

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Macromolecule #3: Structural maintenance of chromosomes protein 1

MacromoleculeName: Structural maintenance of chromosomes protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 140.728953 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGRLLRLEVE NFKSYRGHQI IGPFEDFTSI IGPNGAGKSN LMDAISFVLG VKSSHLRSTN VKELIYRGKI LQRDNTDFTD SSNPTTAYV KLMYELDNGE QREYKRAITP SGATEYKIDE EIVTFSEYCG SLQKENILVR ARNFLVFQGD VETIASQSPL E LSKLVEQI ...String:
MGRLLRLEVE NFKSYRGHQI IGPFEDFTSI IGPNGAGKSN LMDAISFVLG VKSSHLRSTN VKELIYRGKI LQRDNTDFTD SSNPTTAYV KLMYELDNGE QREYKRAITP SGATEYKIDE EIVTFSEYCG SLQKENILVR ARNFLVFQGD VETIASQSPL E LSKLVEQI SGSLEYKSEY DKSKDEQDKA VNLSAHSFNK KRGINAELRQ YQEQKTEAER YQSQKEKRDS AQLVYLLWKL FH LEKSISS NMAEVTRLKA DSIQLIERRD ENTKEIEKLK EKEGSIRRNL LAFDRKVRKQ EKLIASKRPE LISIAEKALE SKS NLRKIQ RKAAEIEKDY SDQASTLQVL ENQLTSLSAA EKEFLKDMQE KEQLKGLRLL PEDKEEYEGL RSEADKLNSN LLFK LQTLN RNIKVTSQSK DSLTSIVGDL ESKIKSLHES VSSLDTERAD LLAKINEKIE SLELEKHDQQ KKRLTYSELF HKTQE LNEE LQSCLQKILE ASADRNESKQ DAKKREALYA LKRIYPEVKG RIIDLCTPTQ KKYESAIAAA LGKNFDAIVV ETQAVA KEC IDYIKEQRIG IMTFFPMDTI AASPVNQKFR GTHKGARLAI DVLNFESEYE RVMISAVGNT LICDSMTVAR DLSYNKR LN AKTVTLEGTV IHKTGLITGG SSNNRSAKHW DDHDFDLLTQ TKDRLMHQIG EIEYQKSSCV ITESDTVKLH SLESEISL L KDKYTVVSRS VEDKKKEIGH YESLIKEKQP HLSELEMELR NFVKSRDELQ IQVEKVEEKI FSGFCKRIGI SDIHTYDEI HRTFTQSFTQ KQLEFTKQKS LLENRISFEK QRVSDTRLRL ERMHKFIEKD QESIDNYEQN REALESEVAT AEAELELLKE DFASENSKT EKILLAASEK KLVGKRLVSE LTKLSGNITL LESEIDRYVS EWHAILRKCK LEDIDVPLRE GSLTSIPIDD V SNSGDITM GEEPSEPVIN FEKFGVEVDY DELDEELRND GSESMASVLQ EKLREYSEEL DQMSPNLRAI ERLETVETRL AK LDEEFAA ARKAAKNAKE RFNAVKQKRL QKFQAAFSHI SEQIDPIYKE LTKSPAFPLG GTAYLTLDDL DEPYLGGIKF HAM PPMKRF RDMDQLSGGE KTMAALALLF AIHSYQPSPF FVLDEIDAAL DQTNVTKIAN YIRQHASSGF QFVVISLKNQ LFSK SEALV GIYRDQQENS SRTLSINLEG YVE

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Macromolecule #4: Structural maintenance of chromosomes protein 3

MacromoleculeName: Structural maintenance of chromosomes protein 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Molecular weightTheoretical: 137.048344 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MYITKIVIQG FKSYKDYTVI EPLSPHHNVI VGRNGSGKSN FFAAIRFVLS DAYTHLSREE RQALLHEGPG ATVMSAYVEV TFANADNRF PTGKSEVVLR RTIGLKKDEY SLDKKTVSKT EVINLLESAG FSRSNPYYIV PQGRVTSLTN AKDSERLELL K EVAGTQIY ...String:
MYITKIVIQG FKSYKDYTVI EPLSPHHNVI VGRNGSGKSN FFAAIRFVLS DAYTHLSREE RQALLHEGPG ATVMSAYVEV TFANADNRF PTGKSEVVLR RTIGLKKDEY SLDKKTVSKT EVINLLESAG FSRSNPYYIV PQGRVTSLTN AKDSERLELL K EVAGTQIY ENRRAESNKI MDETIQKSEK IDELLQYIEE RLRELEEEKN DLAVYHKKDN ERRCLEYAIY SREHDEINSV LD ALEQDRI AALERNDDDS GAFIQREERI ERIKAEITEL NHSLELLRVE KQQNDEDYTN IMKSKVALEL QSSQLSRQIE FSK KDESSK LNILSELESK ISEKENELSE ILPKYNAIVS EADDLNKRIM LLKNQKQSLL DKQSRTSQFT TKKERDEWIR NQLL QINRN INSTKENSDY LKTEYDEMEN ELKAKLSRKK EIEISLESQG DRMSQLLANI TSINERKENL TDKRKSLWRE EAKLK SSIE NVKDDLSRSE KALGTTMDRN TSNGIRAVKD IAERLKLEGY YGPLCELFKV DNRFKVAVEA TAGNSLFHIV VDNDET ATQ ILDVIYKENA GRVTFMPLNK LRPKAVTYPD ASDALPLIQY LEFDPKFDAA IKQVFSKTIV CPSIETASQY ARSHQLN GI TLSGDRSDKK GALTAGYRDY RNSRLDAIKN VKTYQIKFSD LQESLEKCRS EIESFDQKIT ACLDDLQKAQ LSLKQFER D HIPLKDELVT ITGETTDLQE SMHHKSRMLE LVVLELHTLE QQANDLKSEL SSEMDELDPK DVEALKSLSG QIENLSHEF DAIIKERAHI EARKTALEYE LNTNLYLRRN PLKAEIGSDN RIDESELNSV KRSLLKYENK LQIIKSSSSG LEEQMQRINS EISDKRNEL ESLEELQHEV ATRIEQDAKI NERNAAKRSL LLARKKECNE KIKSLGVLPE EAFIKYVSTS SNAIVKKLHK I NEALKDYG SVNKKAYEQF NNFTKQRDSL LARREELRRS QESISELTTV LDQRKDEAIE RTFKQVAKSF SEIFVKLVPA GR GELVMNR RSELSQSIEQ DISMDIDTPS QKSSIDNYTG ISIRVSFNSK DDEQLNINQL SGGQKSLCAL TLIFAIQRCD PAP FNILDE CDANLDAQYR SAIAAMVKEM SKTSQFICTT FRPEMVKVAD NFYGVMFNHK VSTVESISKE EAMAFVEG

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Macromolecule #5: DNA (32-MER)

MacromoleculeName: DNA (32-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.852384 KDa
SequenceString:
(DC)(DA)(DG)(DC)(DA)(DC)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DT)(DA)(DA)(DA)(DA)(DC)(DG) (DA)(DT)(DT)(DG)(DA)(DG)(DA)(DC)(DA) (DC)(DA)(DC)

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Macromolecule #6: DNA (32-MER)

MacromoleculeName: DNA (32-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.82931 KDa
SequenceString:
(DG)(DT)(DG)(DT)(DG)(DT)(DC)(DT)(DC)(DA) (DA)(DT)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DC) (DA)(DA)(DC)(DG)(DT)(DC)(DG)(DT)(DG) (DC)(DT)(DG)

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Macromolecule #7: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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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
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: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 33.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 883184
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 255148

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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