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- EMDB-23818: Cryo-EM 3D map of the S. cerevisiae origin recognition complex bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-23818
TitleCryo-EM 3D map of the S. cerevisiae origin recognition complex bound to Cdc6 and ARS1 origin DNA
Map data
Sample
  • Complex: Complex of origin replication complex with Cdc6 and ARS1 origin 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
    • Protein or peptide: Cell division control protein 6
    • DNA: ARS1 DNA(85-mer)
    • DNA: ARS1 DNA(85-mer)
Function / homology
Function and homology information


CDK-mediated phosphorylation and removal of Cdc6 / CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex ...CDK-mediated phosphorylation and removal of Cdc6 / CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / Cul8-RING ubiquitin ligase complex / maintenance of rDNA / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / 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 / regulation of DNA-templated DNA replication initiation / DNA replication origin binding / regulation of DNA replication / subtelomeric heterochromatin formation / DNA replication initiation / nucleosome binding / G1/S transition of mitotic cell cycle / chromosome / chromosome, telomeric region / cell division / GTPase activity / chromatin binding / GTP binding / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Origin recognition complex, subunit 6, fungi / Cell division protein Cdc6/18 / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / AAA domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 ...Origin recognition complex, subunit 6, fungi / Cell division protein Cdc6/18 / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / AAA domain / 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 (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 / AAA ATPase domain / Origin recognition complex subunit 2 / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / EF-Hand 1, calcium-binding site / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding 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 control protein 6 / 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: 3.3 Å
AuthorsFeng X / Li H
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM45436 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S001387.1 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N000323/1 United States
CitationJournal: Nat Commun / Year: 2021
Title: The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6.
Authors: Xiang Feng / Yasunori Noguchi / Marta Barbon / Bruce Stillman / Christian Speck / Huilin Li /
Abstract: The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell ...The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC-Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins.
History
DepositionApr 10, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateAug 4, 2021-
Current statusAug 4, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mca
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23818.png

Downloads & links

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Map

FileDownload / File: emd_23818.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.0791229 - 0.1127703
Average (Standard dev.)0.00031491992 (±0.003283984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 231.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8280.8280.828
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z231.840231.840231.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0790.1130.000

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Supplemental data

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Half map: #1

Fileemd_23818_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_23818_half_map_2.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 : Complex of origin replication complex with Cdc6 and ARS1 origin DNA

EntireName: Complex of origin replication complex with Cdc6 and ARS1 origin DNA
Components
  • Complex: Complex of origin replication complex with Cdc6 and ARS1 origin 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
    • Protein or peptide: Cell division control protein 6
    • DNA: ARS1 DNA(85-mer)
    • DNA: ARS1 DNA(85-mer)

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Supramolecule #1: Complex of origin replication complex with Cdc6 and ARS1 origin DNA

SupramoleculeName: Complex of origin replication complex with Cdc6 and ARS1 origin DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus / Recombinant cell: Hi-5 cell / Recombinant plasmid: pAcUW51
Molecular weightTheoretical: 470 KDa

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Macromolecule #1: Origin recognition complex subunit 1

MacromoleculeName: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MAKTLKDLQG WEIITTDEQG NIIDGGQKRL RRRGAKTEHY LKRSSDGIKL GRGDSVVMHN EAAGTYSVY MIQELRLNTL NNVVELWALT YLRWFEVNPL AHYRQFNPDA NILNRPLNYY N KLFSETAN KNELYLTAEL AELQLFNFIR VANVMDGSKW EVLKGNVDPE ...String:
MAKTLKDLQG WEIITTDEQG NIIDGGQKRL RRRGAKTEHY LKRSSDGIKL GRGDSVVMHN EAAGTYSVY MIQELRLNTL NNVVELWALT YLRWFEVNPL AHYRQFNPDA NILNRPLNYY N KLFSETAN KNELYLTAEL AELQLFNFIR VANVMDGSKW EVLKGNVDPE RDFTVRYICE PT GEKFVDI NIEDVKAYIK KVEPREAQEY LKDLTLPSKK KEIKRGPQKK DKATQTAQIS DAE TRATDI TDNEDGNEDE SSDYESPSDI DVSEDMDSGE ISADELEEEE DEEEDEDEEE KEAR HTNSP RKRGRKIKLG KDDIDASVQP PPKKRGRKPK DPSKPRQMLL ISSCRANNTP VIRKF TKKN VARAKKKYTP FSKRFKSIAA IPDLTSLPEF YGNSSELMAS RFENKLKTTQ KHQIVE TIF SKVKKQLNSS YVKEEILKSA NFQDYLPARE NEFASIYLSA YSAIESDSAT TIYVAGT PG VGKTLTVREV VKELLSSSAQ REIPDFLYVE INGLKMVKPT DCYETLWNKV SGERLTWA A SMESLEFYFK RVPKNKKKTI VVLLDELDAM VTKSQDIMYN FFNWTTYENA KLIVIAVAN TMDLPERQLG NKITSRIGFT RIMFTGYTHE ELKNIIDLRL KGLNDSFFYV DTKTGNAILI DAAGNDTTV KQTLPEDVRK VRLRMSADAI EIASRKVASV SGDARRALKV CKRAAEIAEK H YMAKHGYG YDGKTVIEDE NEEQIYDDED KDLIESNKAK DDNDDDDDND GVQTVHITHV MK ALNETLN SHVITFMTRL SFTAKLFIYA LLNLMKKNGS QEQELGDIVD EIKLLIEVNG SNK FVMEIA KTLFQQGSDN ISEQLRIISW DFVLNQLLDA GILFKQTMKN DRICCVKLNI SVEE AKRAM NEDETLRNL

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Macromolecule #2: Origin recognition complex subunit 2

MacromoleculeName: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MLNGEDFVEH NDILSSPAKS RNVTPKRVDP HGERQLRRIH SSKKNLLERI SLVGNERKNT SPDPALKPK TPSKAPRKRG RPRKIQEELT DRIKKDEKDT ISSKKKRKLD KDTSGNVNEE S KTSNNKQV MEKTGIKEKR EREKIQVATT TYEDNVTPQT DDNFVSNSPE ...String:
MLNGEDFVEH NDILSSPAKS RNVTPKRVDP HGERQLRRIH SSKKNLLERI SLVGNERKNT SPDPALKPK TPSKAPRKRG RPRKIQEELT DRIKKDEKDT ISSKKKRKLD KDTSGNVNEE S KTSNNKQV MEKTGIKEKR EREKIQVATT TYEDNVTPQT DDNFVSNSPE PPEPATPSKK SL TTNHDFT SPLKQIIMNN LKEYKDSTSP GKLTLSRNFT PTPVPKNKKL YQTSETKSAS SFL DTFEGY FDQRKIVRTN AKSRHTMSMA PDVTREEFSL VSNFFNENFQ KRPRQKLFEI QKKM FPQYW FELTQGFSLL FYGVGSKRNF LEEFAIDYLS PKIAYSQLAY ENELQQNKPV NSIPC LILN GYNPSCNYRD VFKEITDLLV PAELTRSETK YWGNHVILQI QKMIDFYKNQ PLDIKL ILV VHNLDGPSIR KNTFQTMLSF LSVIRQIAIV ASTDHIYAPL LWDNMKAQNY NFVFHDI SN FEPSTVESTF QDVMKMGKSD TSSGAEGAKY VLQSLTVNSK KMYKLLIETQ MQNMGNLS A NTGPKRGTQR TGVELKLFNH LCAADFIASN EIALRSMLRE FIEHKMANIT KNNSGMEII WVPYTYAELE KLLKTVLNTL

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Macromolecule #3: Origin recognition complex subunit 3

MacromoleculeName: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MSDLNQSKKM NVSEFADAQR SHYTVYPSLP QSNKNDKHIP FVKLLSGKES EVNVEKRWEL YHQLHSHFH DQVDHIIDNI EADLKAEISD LLYSETTQKR RCFNTIFLLG SDSTTKIELK D ESSRYNVL IELTPKESPN VRMMLRRSMY KLYSAADAEE HPTIKYEDIN ...String:
MSDLNQSKKM NVSEFADAQR SHYTVYPSLP QSNKNDKHIP FVKLLSGKES EVNVEKRWEL YHQLHSHFH DQVDHIIDNI EADLKAEISD LLYSETTQKR RCFNTIFLLG SDSTTKIELK D ESSRYNVL IELTPKESPN VRMMLRRSMY KLYSAADAEE HPTIKYEDIN DEDGDFTEQN ND VSYDLSL VENFKRLFGK DLAMVFNFKD VDSINFNTLD NFIILLKSAF KYDHVKISLI FNI NTNLSN IEKNLRQSTI RLLKRNYHKL DVSSNKGFKY GNQIFQSFLD TVDGKLNLSD RFVE FILSK MANNTNHNLQ LLTKMLDYSL MSYFFQNAFS VFIDPVNVDF LNDDYLKILS RCPTF MFFV EGLIKQHAPA DEILSLLTNK NRGLEEFFVE FLVRENPING HAKFVARFLE EELNIT NFN LIELYHNLLI GKLDSYLDRW SACKEYKDRL HFEPIDTIFQ ELFTLDNRSG LLTQSIF PS YKSNIEDNLL SWEQVLPSLD KENYDTLSGD LDKIMAPVLG QLFKLYREAN MTINIYDF Y IAFRETLPKE EILNFIRKDP SNTKLLELAE TPDAFDKVAL ILFMQAIFAF ENMGLIKFQ STKSYDLVEK CVWRGI

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Macromolecule #4: Origin recognition complex subunit 4

MacromoleculeName: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MTISEARLSP QVNLLPIKRH SNEEVEETAA ILKKRTIDNE KCKDSDPGFG SLQRRLLQQL YGTLPTDEK IIFTYLQDCQ QEIDRIIKQS IIQKESHSVI LVGPRQSYKT YLLDYELSLL Q QSYKEQFI TIRLNGFIHS EQTAINGIAT QLEQQLQKIH GSEEKIDDTS ...String:
MTISEARLSP QVNLLPIKRH SNEEVEETAA ILKKRTIDNE KCKDSDPGFG SLQRRLLQQL YGTLPTDEK IIFTYLQDCQ QEIDRIIKQS IIQKESHSVI LVGPRQSYKT YLLDYELSLL Q QSYKEQFI TIRLNGFIHS EQTAINGIAT QLEQQLQKIH GSEEKIDDTS LETISSGSLT EV FEKILLL LDSTTKTRNE DSGEVDRESI TKITVVFIFD EIDTFAGPVR QTLLYNLFDM VEH SRVPVC IFGCTTKLNI LEYLEKRVKS RFSQRVIYMP QIQNLDDMVD AVRNLLTVRS EISP WVSQW NETLEKELSD PRSNLNRHIR MNFETFRSLP TLKNSIIPLV ATSKNFGSLC TAIKS CSFL DIYNKNQLSN NLTGRLQSLS DLELAILISA ARVALRAKDG SFNFNLAYAE YEKMIK AIN SRIPTVAPTT NVGTGQSTFS IDNTIKLWLK KDVKNVWENL VQLDFFTEKS AVGLRDN AT AAFYASNYQF QGTMIPFDLR SYQMQIILQE LRRIIPKSNM YYSWTQL

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Macromolecule #5: Origin recognition complex subunit 5

MacromoleculeName: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MNVTTPEVAF REYQTNCLAS YISADPDITP SNLILQGYSG TGKTYTLKKY FNANPNLHAV WLEPVELVS WKPLLQAIAR TVQYKLKTLY PNIPTTDYDP LQVEEPFLLV KTLHNIFVQY E SLQEKTCL FLILDGFDSL QDLDAALFNK YIKLNELLPK DSKINIKFIY ...String:
MNVTTPEVAF REYQTNCLAS YISADPDITP SNLILQGYSG TGKTYTLKKY FNANPNLHAV WLEPVELVS WKPLLQAIAR TVQYKLKTLY PNIPTTDYDP LQVEEPFLLV KTLHNIFVQY E SLQEKTCL FLILDGFDSL QDLDAALFNK YIKLNELLPK DSKINIKFIY TMLETSFLQR YS THCIPTV MFPRYNVDEV STILVMSRCG ELMEDSCLRK RIIEEQITDC TDDQFQNVAA NFI HLIVQA FHSYTGNDIF ALNDLIDFKW PKYVSRITKE NIFEPLALYK SAIKLFLSTD DNLS ENGQG ESAITTNRDD LENSQTYDLS IISKYLLIAS YICSYLEPRY DASIFSRKTR IIQGR AAYG RRKKKEVNPR YLQPSLFAIE RLLAIFQAIF PIQGKAESGS LSALREESLM KANIEV FQN LSELHTLKLI ATTMNKNIDY LSPKVRWKVN VPWEIIKEIS ESVHFNISDY FSDIHE

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Macromolecule #6: Origin recognition complex subunit 6

MacromoleculeName: Origin recognition complex subunit 6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MSMQQVQHCV AEVLRLDPQE KPDWSSGYLK KLTNATSILY NTSLNKVMLK QDEEVARCHI CAYIASQKM NEKHMPDLCY YIDSIPLEPK KAKHLMNLFR QSLSNSSPMK QFAWTPSPKK N KRSPVKNG GRFTSSDPKE LRNQLFGTPT KVRKSQNNDS FVIPELPPMQ ...String:
MSMQQVQHCV AEVLRLDPQE KPDWSSGYLK KLTNATSILY NTSLNKVMLK QDEEVARCHI CAYIASQKM NEKHMPDLCY YIDSIPLEPK KAKHLMNLFR QSLSNSSPMK QFAWTPSPKK N KRSPVKNG GRFTSSDPKE LRNQLFGTPT KVRKSQNNDS FVIPELPPMQ TNESPSITRR KL AFEEDED EDEEEPGNDG LSLKSHSNKS ITGTRNVDSD EYENHESDPT SEEEPLGVQE SRS GRTKQN KAVGKPQSEL KTAKALRKRG RIPNSLLVKK YCKMTTEEII RLCNDFELPR EVAY KIVDE YNINASRLVC PWQLVCGLVL NCTFIVFNER RRKDPRIDHF IVSKMCSLML TSKVD DVIE CVKLVKELII GEKWFRDLQI RYDDFDGIRY DEIIFRKLGS MLQTTNILVT DDQYNI WKK RIEMDLALTE PL

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Macromolecule #7: Cell division control protein 6

MacromoleculeName: Cell division control protein 6 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MSAIPITPTK RIRRNLFDDA PATPPRPLKR KKLQFTDVTP ESSPEKLQFG SQSIFLRTKA LLQKSSELV NLNSSDGALP ARTAEYEQVM NFLAKAISEH RSDSLYITGP PGTGKTAQLD M IIRQKFQS LPLSLSTPRS KDVLRHTNPN LQNLSWFELP DGRLESVAVT ...String:
MSAIPITPTK RIRRNLFDDA PATPPRPLKR KKLQFTDVTP ESSPEKLQFG SQSIFLRTKA LLQKSSELV NLNSSDGALP ARTAEYEQVM NFLAKAISEH RSDSLYITGP PGTGKTAQLD M IIRQKFQS LPLSLSTPRS KDVLRHTNPN LQNLSWFELP DGRLESVAVT SINCISLGEP SS IFQKIFD SFQDLNGPTL QIKNMQHLQK FLEPYHKKTT FVVVLDEMDR LLHANTSETQ SVR TILELF LLAKLPTVSF VLIGMANSLD MKDRFLSRLN LDRGLLPQTI VFQPYTAEQM YEIV IQKMS SLPTIIFQPM AIKFAAKKCA GNTGDLRKLF DVLRGSIEIY ELEKRFLLSP TRGSL NSAQ VPLTPTTSPV KKSYPEPQGK IGLNYIAKVF SKFVNNNSTR TRIAKLNIQQ KLILCT IIQ SLKLNSDATI DESFDHYIKA ITKTDTLAPL QRNEFLEICT ILETCGLVSI KKTKCKG KT KRFVDKIDVD LDMREFYDEM TKISILKPFL H

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Macromolecule #8: ARS1 DNA(85-mer)

MacromoleculeName: ARS1 DNA(85-mer) / type: dna / ID: 8 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: (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) ...String:
(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)(DC)(DA)(DA)(DT)(DA)(DC) (DT)(DT)(DA) (DA)(DA)(DT)(DA)(DA)

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Macromolecule #9: ARS1 DNA(85-mer)

MacromoleculeName: ARS1 DNA(85-mer) / type: dna / ID: 9 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: (DT)(DT)(DA)(DT)(DT)(DT)(DA)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(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) ...String:
(DT)(DT)(DA)(DT)(DT)(DT)(DA)(DA)(DG)(DT) (DA)(DT)(DT)(DG)(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)

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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
Component:
ConcentrationFormulaName
50.0 mMHEPES
100.0 mMCH3CO2Kpotassium acetate
5.0 mMC4H6MgO4magnesium acetate
5.0 mMATP-gamma-S
2.0 mMDTT
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 K3 (6k x 4k) / Average electron dose: 76.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 177397
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Startup modelType of model: INSILICO MODEL / In silico model: cryosparc ab initio reconstruction
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 2 / Avg.num./class: 1 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 264117

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Atomic model buiding 1

Initial modelPDB ID:

5v8f

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 118.5 / Target criteria: correlation coefficient
Output model

PDB-7mca:
Structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA.

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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