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- EMDB-25924: S. cerevisiae ORC bound to 84 bp ARS1 DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-25924
TitleS. cerevisiae ORC bound to 84 bp ARS1 DNA
Map dataunsharpened cryo-EM map
Sample
  • Complex: ORC in complex with ARS1 DNA
    • Protein or peptide: x 6 types
    • DNA: x 2 types
  • Ligand: x 3 types
Keywordsinitiator / helicase loader / AAA+ ATPase / REPLICATION-DNA complex
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / Activation of ATR in response to replication stress ...CDC6 association with the ORC:origin complex / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nucleosome organization / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / Orc1 removal from chromatin / regulation of DNA replication / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / nucleosome binding / chromosome, telomeric region / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
Origin recognition complex, subunit 6, fungi / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal ...Origin recognition complex, subunit 6, fungi / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 3, N-terminal / : / : / Origin recognition complex (ORC) subunit 3 N-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex winged helix C-terminal / ORC5, lid domain / Orc1-like, AAA ATPase domain / Origin recognition complex subunit 2 RecA-like domain / AAA ATPase domain / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / EF-Hand 1, calcium-binding site / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Origin recognition complex subunit 2 / Origin recognition complex subunit 6 / Origin recognition complex subunit 5 / Origin recognition complex subunit 1 / Origin recognition complex subunit 3 / Origin recognition complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSchmidt JM / Yang R
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM141313 United States
European Research Council (ERC)ERC-STG-757909 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008283 United States
CitationJournal: Nat Commun / Year: 2022
Title: A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6.
Authors: Jan Marten Schmidt / Ran Yang / Ashish Kumar / Olivia Hunker / Jan Seebacher / Franziska Bleichert /
Abstract: The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to ...The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to DNA initiates the ATP-dependent recruitment of Cdc6, Cdt1 and Mcm2-7 loading, but the structural details for timely ATPase site regulation and for how loading can be impeded by inhibitory signals, such as cyclin-dependent kinase phosphorylation, are unknown. Using cryo-electron microscopy, we have determined several structures of S. cerevisiae ORC·DNA·Cdc6 intermediates at 2.5-2.7 Å resolution. These structures reveal distinct ring conformations of the initiator·co-loader assembly and inactive ATPase site configurations for ORC and Cdc6. The Orc6 N-terminal domain laterally engages the ORC·Cdc6 ring in a manner that is incompatible with productive Mcm2-7 docking, while deletion of this Orc6 region alleviates the CDK-mediated inhibition of Mcm7 recruitment. Our findings support a model in which Orc6 promotes the assembly of an autoinhibited ORC·DNA·Cdc6 intermediate to block origin licensing in response to CDK phosphorylation and to avert DNA re-replication.
History
DepositionJan 16, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25924.png

Downloads & links

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Map

FileDownload / File: emd_25924.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.024002442 - 0.08941924
Average (Standard dev.)-0.000002157307 (±0.0022276894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened, masked cryo-EM map

Fileemd_25924_additional_1.map
Annotationsharpened, masked cryo-EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: density modified cryo-EM map

Fileemd_25924_additional_2.map
Annotationdensity modified cryo-EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_25924_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_25924_half_map_2.map
Annotationhalf 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 : ORC in complex with ARS1 DNA

EntireName: ORC in complex with ARS1 DNA
Components
  • Complex: ORC in complex with ARS1 DNA
    • Protein or peptide: Origin recognition complex subunit 1
    • Protein or peptide: Origin recognition complex subunit 2
    • Protein or peptide: Origin recognition complex subunit 3
    • Protein or peptide: Origin recognition complex subunit 4
    • Protein or peptide: Origin recognition complex subunit 5
    • Protein or peptide: Origin recognition complex subunit 6
    • DNA: DNA, 84 bp ARS1
    • DNA: DNA, 84 bp ARS1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: ORC in complex with ARS1 DNA

SupramoleculeName: ORC in complex with ARS1 DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Macromolecule #1: Origin recognition complex subunit 1

MacromoleculeName: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 104.818422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMAKTLKD LQGWEIITTD EQGNIIDGGQ KRLRRRGAKT EHYLKRSSDG IKLGRGDSVV MHNEAAGTYS VYMIQELRLN TLNNVVELW ALTYLRWFEV NPLAHYRQFN PDANILNRPL NYYNKLFSET ANKNELYLTA ELAELQLFNF IRVANVMDGS K WEVLKGNV ...String:
SNAMAKTLKD LQGWEIITTD EQGNIIDGGQ KRLRRRGAKT EHYLKRSSDG IKLGRGDSVV MHNEAAGTYS VYMIQELRLN TLNNVVELW ALTYLRWFEV NPLAHYRQFN PDANILNRPL NYYNKLFSET ANKNELYLTA ELAELQLFNF IRVANVMDGS K WEVLKGNV DPERDFTVRY ICEPTGEKFV DINIEDVKAY IKKVEPREAQ EYLKDLTLPS KKKEIKRGPQ KKDKATQTAQ IS DAETRAT DITDNEDGNE DESSDYESPS DIDVSEDMDS GEISADELEE EEDEEEDEDE EEKEARHTNS PRKRGRKIKL GKD DIDASV QPPPKKRGRK PKDPSKPRQM LLISSCRANN TPVIRKFTKK NVARAKKKYT PFSKRFKSIA AIPDLTSLPE FYGN SSELM ASRFENKLKT TQKHQIVETI FSKVKKQLNS SYVKEEILKS ANFQDYLPAR ENEFASIYLS AYSAIESDSA TTIYV AGTP GVGKTLTVRE VVKELLSSSA QREIPDFLYV EINGLKMVKP TDCYETLWNK VSGERLTWAA SMESLEFYFK RVPKNK KKT IVVLLDELDA MVTKSQDIMY NFFNWTTYEN AKLIVIAVAN TMDLPERQLG NKITSRIGFT RIMFTGYTHE ELKNIID LR LKGLNDSFFY VDTKTGNAIL IDAAGNDTTV KQTLPEDVRK VRLRMSADAI EIASRKVASV SGDARRALKV CKRAAEIA E KHYMAKHGYG YDGKTVIEDE NEEQIYDDED KDLIESNKAK DDNDDDDDND GVQTVHITHV MKALNETLNS HVITFMTRL SFTAKLFIYA LLNLMKKNGS QEQELGDIVD EIKLLIEVNG SNKFVMEIAK TLFQQGSDNI SEQLRIISWD FVLNQLLDAG ILFKQTMKN DRICCVKLNI SVEEAKRAMN EDETLRNL

UniProtKB: Origin recognition complex subunit 1

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Macromolecule #2: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 71.34218 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLNGEDFVEH NDILSSPAKS RNVTPKRVDP HGERQLRRIH SSKKNLLERI SLVGNERKNT SPDPALKPKT PSKAPRKRGR PRKIQEELT DRIKKDEKDT ISSKKKRKLD KDTSGNVNEE SKTSNNKQVM EKTGIKEKRE REKIQVATTT YEDNVTPQTD D NFVSNSPE ...String:
MLNGEDFVEH NDILSSPAKS RNVTPKRVDP HGERQLRRIH SSKKNLLERI SLVGNERKNT SPDPALKPKT PSKAPRKRGR PRKIQEELT DRIKKDEKDT ISSKKKRKLD KDTSGNVNEE SKTSNNKQVM EKTGIKEKRE REKIQVATTT YEDNVTPQTD D NFVSNSPE PPEPATPSKK SLTTNHDFTS PLKQIIMNNL KEYKDSTSPG KLTLSRNFTP TPVPKNKKLY QTSETKSASS FL DTFEGYF DQRKIVRTNA KSRHTMSMAP DVTREEFSLV SNFFNENFQK RPRQKLFEIQ KKMFPQYWFE LTQGFSLLFY GVG SKRNFL EEFAIDYLSP KIAYSQLAYE NELQQNKPVN SIPCLILNGY NPSCNYRDVF KEITDLLVPA ELTRSETKYW GNHV ILQIQ KMIDFYKNQP LDIKLILVVH NLDGPSIRKN TFQTMLSFLS VIRQIAIVAS TDHIYAPLLW DNMKAQNYNF VFHDI SNFE PSTVESTFQD VMKMGKSDTS SGAEGAKYVL QSLTVNSKKM YKLLIETQMQ NMGNLSANTG PKRGTQRTGV ELKLFN HLC AADFIASNEI ALRSMLREFI EHKMANITKN NSGMEIIWVP YTYAELEKLL KTVLNTL

UniProtKB: Origin recognition complex subunit 2

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Macromolecule #3: Origin recognition complex subunit 3

MacromoleculeName: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 72.161766 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSDLNQSKKM NVSEFADAQR SHYTVYPSLP QSNKNDKHIP FVKLLSGKES EVNVEKRWEL YHQLHSHFHD QVDHIIDNIE ADLKAEISD LLYSETTQKR RCFNTIFLLG SDSTTKIELK DESSRYNVLI ELTPKESPNV RMMLRRSMYK LYSAADAEEH P TIKYEDIN ...String:
MSDLNQSKKM NVSEFADAQR SHYTVYPSLP QSNKNDKHIP FVKLLSGKES EVNVEKRWEL YHQLHSHFHD QVDHIIDNIE ADLKAEISD LLYSETTQKR RCFNTIFLLG SDSTTKIELK DESSRYNVLI ELTPKESPNV RMMLRRSMYK LYSAADAEEH P TIKYEDIN DEDGDFTEQN NDVSYDLSLV ENFKRLFGKD LAMVFNFKDV DSINFNTLDN FIILLKSAFK YDHVKISLIF NI NTNLSNI EKNLRQSTIR LLKRNYHKLD VSSNKGFKYG NQIFQSFLDT VDGKLNLSDR FVEFILSKMA NNTNHNLQLL TKM LDYSLM SYFFQNAFSV FIDPVNVDFL NDDYLKILSR CPTFMFFVEG LIKQHAPADE ILSLLTNKNR GLEEFFVEFL VREN PINGH AKFVARFLEE ELNITNFNLI ELYHNLLIGK LDSYLDRWSA CKEYKDRLHF EPIDTIFQEL FTLDNRSGLL TQSIF PSYK SNIEDNLLSW EQVLPSLDKE NYDTLSGDLD KIMAPVLGQL FKLYREANMT INIYDFYIAF RETLPKEEIL NFIRKD PSN TKLLELAETP DAFDKVALIL FMQAIFAFEN MGLIKFQSTK SYDLVEKCVW RGI

UniProtKB: Origin recognition complex subunit 3

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Macromolecule #4: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 61.044414 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMTISEAR LSPQVNLLPI KRHSNEEVEE TAAILKKRTI DNEKCKDSDP GFGSLQRRLL QQLYGTLPTD EKIIFTYLQD CQQEIDRII KQSIIQKESH SVILVGPRQS YKTYLLDYEL SLLQQSYKEQ FITIRLNGFI HSEQTAINGI ATQLEQQLQK I HGSEEKID ...String:
SNAMTISEAR LSPQVNLLPI KRHSNEEVEE TAAILKKRTI DNEKCKDSDP GFGSLQRRLL QQLYGTLPTD EKIIFTYLQD CQQEIDRII KQSIIQKESH SVILVGPRQS YKTYLLDYEL SLLQQSYKEQ FITIRLNGFI HSEQTAINGI ATQLEQQLQK I HGSEEKID DTSLETISSG SLTEVFEKIL LLLDSTTKTR NEDSGEVDRE SITKITVVFI FDEIDTFAGP VRQTLLYNLF DM VEHSRVP VCIFGCTTKL NILEYLEKRV KSRFSQRVIY MPQIQNLDDM VDAVRNLLTV RSEISPWVSQ WNETLEKELS DPR SNLNRH IRMNFETFRS LPTLKNSIIP LVATSKNFGS LCTAIKSCSF LDIYNKNQLS NNLTGRLQSL SDLELAILIS AARV ALRAK DGSFNFNLAY AEYEKMIKAI NSRIPTVAPT TNVGTGQSTF SIDNTIKLWL KKDVKNVWEN LVQLDFFTEK SAVGL RDNA TAAFYASNYQ FQGTMIPFDL RSYQMQIILQ ELRRIIPKSN MYYSWTQL

UniProtKB: Origin recognition complex subunit 4

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Macromolecule #5: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 55.347168 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNVTTPEVAF REYQTNCLAS YISADPDITP SNLILQGYSG TGKTYTLKKY FNANPNLHAV WLEPVELVSW KPLLQAIART VQYKLKTLY PNIPTTDYDP LQVEEPFLLV KTLHNIFVQY ESLQEKTCLF LILDGFDSLQ DLDAALFNKY IKLNELLPKD S KINIKFIY ...String:
MNVTTPEVAF REYQTNCLAS YISADPDITP SNLILQGYSG TGKTYTLKKY FNANPNLHAV WLEPVELVSW KPLLQAIART VQYKLKTLY PNIPTTDYDP LQVEEPFLLV KTLHNIFVQY ESLQEKTCLF LILDGFDSLQ DLDAALFNKY IKLNELLPKD S KINIKFIY TMLETSFLQR YSTHCIPTVM FPRYNVDEVS TILVMSRCGE LMEDSCLRKR IIEEQITDCT DDQFQNVAAN FI HLIVQAF HSYTGNDIFA LNDLIDFKWP KYVSRITKEN IFEPLALYKS AIKLFLSTDD NLSENGQGES AITTNRDDLE NSQ TYDLSI ISKYLLIASY ICSYLEPRYD ASIFSRKTRI IQGRAAYGRR KKKEVNPRYL QPSLFAIERL LAIFQAIFPI QGKA ESGSL SALREESLMK ANIEVFQNLS ELHTLKLIAT TMNKNIDYLS PKVRWKVNVP WEIIKEISES VHFNISDYFS DIHE

UniProtKB: Origin recognition complex subunit 5

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Macromolecule #6: Origin recognition complex subunit 6

MacromoleculeName: Origin recognition complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.369531 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSMQQVQHCV AEVLRLDPQE KPDWSSGYLK KLTNATSILY NTSLNKVMLK QDEEVARCHI CAYIASQKMN EKHMPDLCYY IDSIPLEPK KAKHLMNLFR QSLSNSSPMK QFAWTPSPKK NKRSPVKNGG RFTSSDPKEL RNQLFGTPTK VRKSQNNDSF V IPELPPMQ ...String:
MSMQQVQHCV AEVLRLDPQE KPDWSSGYLK KLTNATSILY NTSLNKVMLK QDEEVARCHI CAYIASQKMN EKHMPDLCYY IDSIPLEPK KAKHLMNLFR QSLSNSSPMK QFAWTPSPKK NKRSPVKNGG RFTSSDPKEL RNQLFGTPTK VRKSQNNDSF V IPELPPMQ TNESPSITRR KLAFEEDEDE DEEEPGNDGL SLKSHSNKSI TGTRNVDSDE YENHESDPTS EEEPLGVQES RS GRTKQNK AVGKPQSELK TAKALRKRGR IPNSLLVKKY CKMTTEEIIR LCNDFELPRE VAYKIVDEYN INASRLVCPW QLV CGLVLN CTFIVFNERR RKDPRIDHFI VSKMCSLMLT SKVDDVIECV KLVKELIIGE KWFRDLQIRY DDFDGIRYDE IIFR KLGSM LQTTNILVTD DQYNIWKKRI EMDLALTEPL

UniProtKB: Origin recognition complex subunit 6

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Macromolecule #7: DNA, 84 bp ARS1

MacromoleculeName: DNA, 84 bp ARS1 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.820561 KDa
SequenceString: (DA)(DT)(DC)(DT)(DT)(DT)(DA)(DC)(DA)(DT) (DC)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DT)(DT) (DT)(DA)(DC)(DA)(DG)(DA)(DT)(DT)(DT) (DT)(DA)(DT)(DG)(DT)(DT)(DT)(DA)(DG)(DA) (DT) (DC)(DT)(DT)(DT)(DT)(DA) ...String:
(DA)(DT)(DC)(DT)(DT)(DT)(DA)(DC)(DA)(DT) (DC)(DT)(DT)(DG)(DT)(DT)(DA)(DT)(DT)(DT) (DT)(DA)(DC)(DA)(DG)(DA)(DT)(DT)(DT) (DT)(DA)(DT)(DG)(DT)(DT)(DT)(DA)(DG)(DA) (DT) (DC)(DT)(DT)(DT)(DT)(DA)(DT)(DG) (DC)(DT)(DT)(DG)(DC)(DT)(DT)(DT)(DT)(DC) (DA)(DA) (DA)(DA)(DG)(DG)(DC)(DC)(DT) (DG)(DC)(DA)(DG)(DG)(DC)(DA)(DA)(DG)(DT) (DG)(DC)(DA) (DC)(DA)(DA)(DA)

GENBANK: GENBANK: CP007814.1

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Macromolecule #8: DNA, 84 bp ARS1

MacromoleculeName: DNA, 84 bp ARS1 / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.977766 KDa
SequenceString: (DT)(DT)(DT)(DG)(DT)(DG)(DC)(DA)(DC)(DT) (DT)(DG)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DA) (DA)(DA)(DG)(DC)(DA)(DA)(DG)(DC)(DA)(DT) (DA) (DA)(DA)(DA)(DG)(DA)(DT) ...String:
(DT)(DT)(DT)(DG)(DT)(DG)(DC)(DA)(DC)(DT) (DT)(DG)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DA) (DA)(DA)(DG)(DC)(DA)(DA)(DG)(DC)(DA)(DT) (DA) (DA)(DA)(DA)(DG)(DA)(DT)(DC)(DT) (DA)(DA)(DA)(DC)(DA)(DT)(DA)(DA)(DA)(DA) (DT)(DC) (DT)(DG)(DT)(DA)(DA)(DA)(DA) (DT)(DA)(DA)(DC)(DA)(DA)(DG)(DA)(DT)(DG) (DT)(DA)(DA) (DA)(DG)(DA)(DT)

GENBANK: GENBANK: CP007814.1

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / 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 #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 297 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 6.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238056
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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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