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- EMDB-6941: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72... -

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Basic information

Entry
Database: EMDB / ID: EMD-6941
TitleSaccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Map data
Sample
  • Complex: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
    • 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: 72bp-oring DNA, ACS305, T-rich
    • DNA: 72bp-oring DNA, ACS305, A-rich
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsOrigin Recognition Complex / DNA replication initiation / 72-bp origin DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / 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 / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / 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 / nucleosome binding / DNA replication initiation / subtelomeric heterochromatin formation / 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 / 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) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLi N / Lam WH
CitationJournal: Nature / Year: 2018
Title: Structure of the origin recognition complex bound to DNA replication origin.
Authors: Ningning Li / Wai Hei Lam / Yuanliang Zhai / Jiaxuan Cheng / Erchao Cheng / Yongqian Zhao / Ning Gao / Bik-Kwoon Tye /
Abstract: The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the ...The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element. The ORC encircles DNA through extensive interactions with both phosphate backbone and bases, and bends DNA at the ACS and B1 sites. Specific recognition of thymine residues in the ACS is carried out by a conserved basic amino acid motif of Orc1 in the minor groove, and by a species-specific helical insertion motif of Orc4 in the major groove. Moreover, similar insertions into major and minor grooves are also embedded in the B1 site by basic patch motifs from Orc2 and Orc5, respectively, to contact bases and to bend DNA. This work pinpoints a conserved role of ORC in modulating DNA structure to facilitate origin selection and helicase loading in eukaryotes.
History
DepositionApr 21, 2018-
Header (metadata) releaseJul 11, 2018-
Map releaseJul 11, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-5zr1
  • Surface level: 0.05
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6941.png

Downloads & links

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Map

FileDownload / File: emd_6941.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 269.312 Å		1.05 Å/pix.
x 256 pix.
= 269.312 Å		1.05 Å/pix.
x 256 pix.
= 269.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.19995214 - 0.44266602
Average (Standard dev.)0.0006592716 (±0.010016402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 269.312 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z269.312269.312269.312
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2000.4430.001

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Supplemental data

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Sample components

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Entire : Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72...

EntireName: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Components
  • Complex: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
    • 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: 72bp-oring DNA, ACS305, T-rich
    • DNA: 72bp-oring DNA, ACS305, A-rich
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72...

SupramoleculeName: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Details: Saccharomyces Cerevisiae Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 72-bp Origin DNA (a 72-bp dsDNA chain G-H) containing ACS and B1 element
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 104.546164 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAKTLKDLQG WEIITTDEQG NIIDGGQKRL RRRGAKTEHY LKRSSDGIKL GRGDSVVMHN EAAGTYSVYM IQELRLNTLN NVVELWALT YLRWFEVNPL AHYRQFNPDA NILNRPLNYY NKLFSETANK NELYLTAELA ELQLFNFIRV ANVMDGSKWE V LKGNVDPE ...String:
MAKTLKDLQG WEIITTDEQG NIIDGGQKRL RRRGAKTEHY LKRSSDGIKL GRGDSVVMHN EAAGTYSVYM IQELRLNTLN NVVELWALT YLRWFEVNPL AHYRQFNPDA NILNRPLNYY NKLFSETANK NELYLTAELA ELQLFNFIRV ANVMDGSKWE V LKGNVDPE RDFTVRYICE PTGEKFVDIN IEDVKAYIKK VEPREAQEYL KDLTLPSKKK EIKRGPQKKD KATQTAQISD AE TRATDIT DNEDGNEDES SDYESPSDID VSEDMDSGEI SADELEEEED EEEDEDEEEK EARHTNSPRK RGRKIKLGKD DID ASVQPP PKKRGRKPKD PSKPRQMLLI SSCRANNTPV IRKFTKKNVA RAKKKYTPFS KRFKSIAAIP DLTSLPEFYG NSSE LMASR FENKLKTTQK HQIVETIFSK VKKQLNSSYV KEEILKSANF QDYLPARENE FASIYLSAYS AIESDSATTI YVAGT PGVG KTLTVREVVK ELLSSSAQRE IPDFLYVEIN GLKMVKPTDC YETLWNKVSG ERLTWAASME SLEFYFKRVP KNKKKT IVV LLDELDAMVT KSQDIMYNFF NWTTYENAKL IVIAVANTMD LPERQLGNKI TSRIGFTRIM FTGYTHEELK NIIDLRL KG LNDSFFYVDT KTGNAILIDA AGNDTTVKQT LPEDVRKVRL RMSADAIEIA SRKVASVSGD ARRALKVCKR AAEIAEKH Y MAKHGYGYDG KTVIEDENEE QIYDDEDKDL IESNKAKDDN DDDDDNDGVQ TVHITHVMKA LNETLNSHVI TFMTRLSFT AKLFIYALLN LMKKNGSQEQ ELGDIVDEIK LLIEVNGSNK FVMEIAKTLF QQGSDNISEQ LRIISWDFVL NQLLDAGILF KQTMKNDRI CCVKLNISVE EAKRAMNEDE TLRNL

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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 71.34218 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 72.161766 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 60.772152 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTISEARLSP QVNLLPIKRH SNEEVEETAA ILKKRTIDNE KCKDSDPGFG SLQRRLLQQL YGTLPTDEKI IFTYLQDCQQ EIDRIIKQS IIQKESHSVI LVGPRQSYKT YLLDYELSLL QQSYKEQFIT IRLNGFIHSE QTAINGIATQ LEQQLQKIHG S EEKIDDTS ...String:
MTISEARLSP QVNLLPIKRH SNEEVEETAA ILKKRTIDNE KCKDSDPGFG SLQRRLLQQL YGTLPTDEKI IFTYLQDCQQ EIDRIIKQS IIQKESHSVI LVGPRQSYKT YLLDYELSLL QQSYKEQFIT IRLNGFIHSE QTAINGIATQ LEQQLQKIHG S EEKIDDTS LETISSGSLT EVFEKILLLL DSTTKTRNED SGEVDRESIT KITVVFIFDE IDTFAGPVRQ TLLYNLFDMV EH SRVPVCI FGCTTKLNIL EYLEKRVKSR FSQRVIYMPQ IQNLDDMVDA VRNLLTVRSE ISPWVSQWNE TLEKELSDPR SNL NRHIRM NFETFRSLPT LKNSIIPLVA TSKNFGSLCT AIKSCSFLDI YNKNQLSNNL TGRLQSLSDL ELAILISAAR VALR AKDGS FNFNLAYAEY EKMIKAINSR IPTVAPTTNV GTGQSTFSID NTIKLWLKKD VKNVWENLVQ LDFFTEKSAV GLRDN ATAA FYASNYQFQG TMIPFDLRSY QMQIILQELR RIIPKSNMYY SWTQL

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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.347168 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 50.369531 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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: 72bp-oring DNA, ACS305, T-rich

MacromoleculeName: 72bp-oring DNA, ACS305, T-rich / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.203266 KDa
SequenceString: (DT)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DT)(DG)(DT)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DT) (DT)(DT)(DA)(DT)(DT)(DT)(DT)(DC)(DC)(DC) (DT) (DT)(DT)(DA)(DA)(DT)(DT) ...String:
(DT)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DT)(DG)(DT)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DT) (DT)(DT)(DA)(DT)(DT)(DT)(DT)(DC)(DC)(DC) (DT) (DT)(DT)(DA)(DA)(DT)(DT)(DT)(DT) (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DG)(DA)(DA) (DA)(DA) (DC)(DA)(DA)(DG)(DA)(DA)(DT) (DT)(DT)(DA)(DT)(DC)

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Macromolecule #8: 72bp-oring DNA, ACS305, A-rich

MacromoleculeName: 72bp-oring DNA, ACS305, A-rich / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.174412 KDa
SequenceString: (DG)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DT) (DT)(DG)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DA) (DT)(DC)(DC)(DT)(DA)(DA)(DA)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DA) (DT)(DA)(DA)(DA)(DC)(DA) ...String:
(DG)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DT) (DT)(DG)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DA) (DT)(DC)(DC)(DT)(DA)(DA)(DA)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DA) (DT)(DA)(DA)(DA)(DC)(DA)(DA)(DT) (DA)(DC)(DA)(DT)(DA)(DA)(DC)(DA)(DA)(DA) (DA)(DC) (DA)(DT)(DA)(DT)(DA)(DA)(DA) (DA)(DA)(DC)(DC)(DA)

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Macromolecule #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 9 / Number of copies: 3 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164857
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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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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