+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22363 | |||||||||
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Title | Structure of Drosophila ORC in the active conformation | |||||||||
Map data | unsharpened, unmasked cryo-EM map | |||||||||
Sample |
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Keywords | origin recognition complex / DNA replication initiation / REPLICATION | |||||||||
Function / homology | Function and homology information alpha-heterochromatin / larval feeding behavior / CDC6 association with the ORC:origin complex / septin cytoskeleton / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / origin recognition complex ...alpha-heterochromatin / larval feeding behavior / CDC6 association with the ORC:origin complex / septin cytoskeleton / septin cytoskeleton organization / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / origin recognition complex / DNA amplification / positive regulation of border follicle cell migration / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / olfactory learning / nuclear pre-replicative complex / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / mitotic chromosome condensation / chromosome condensation / DNA replication origin binding / DNA replication initiation / heterochromatin / ribonucleoprotein complex binding / nuclear pore / GTPase activator activity / mitotic spindle organization / learning / DNA-templated DNA replication / mitotic cell cycle / DNA replication / learning or memory / chromatin binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Schmidt JM / Bleichert F | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Authors: Jan Marten Schmidt / Franziska Bleichert / Abstract: Eukaryotic DNA replication initiation relies on the origin recognition complex (ORC), a DNA-binding ATPase that loads the Mcm2-7 replicative helicase onto replication origins. Here, we report cryo- ...Eukaryotic DNA replication initiation relies on the origin recognition complex (ORC), a DNA-binding ATPase that loads the Mcm2-7 replicative helicase onto replication origins. Here, we report cryo-electron microscopy (cryo-EM) structures of DNA-bound Drosophila ORC with and without the co-loader Cdc6. These structures reveal that Orc1 and Orc4 constitute the primary DNA binding site in the ORC ring and cooperate with the winged-helix domains to stabilize DNA bending. A loop region near the catalytic Walker B motif of Orc1 directly contacts DNA, allosterically coupling DNA binding to ORC's ATPase site. Correlating structural and biochemical data show that DNA sequence modulates DNA binding and remodeling by ORC, and that DNA bending promotes Mcm2-7 loading in vitro. Together, these findings explain the distinct DNA sequence-dependencies of metazoan and S. cerevisiae initiators in origin recognition and support a model in which DNA geometry and bendability contribute to Mcm2-7 loading site selection in metazoans. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22363.map.gz | 80.6 MB | EMDB map data format | |
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Header (meta data) | emd-22363-v30.xml emd-22363.xml | 27.3 KB 27.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22363_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_22363.png | 109.3 KB | ||
Filedesc metadata | emd-22363.cif.gz | 8 KB | ||
Others | emd_22363_additional.map.gz emd_22363_half_map_1.map.gz emd_22363_half_map_2.map.gz | 9.5 MB 81 MB 81 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22363 | HTTPS FTP |
-Validation report
Summary document | emd_22363_validation.pdf.gz | 1010 KB | Display | EMDB validaton report |
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Full document | emd_22363_full_validation.pdf.gz | 1009.6 KB | Display | |
Data in XML | emd_22363_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_22363_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22363 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22363 | HTTPS FTP |
-Related structure data
Related structure data | 7jk6MC 7jgrC 7jgsC 7jk2C 7jk3C 7jk4C 7jk5C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22363.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened, unmasked cryo-EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: masked, sharpened cryo-EM map
File | emd_22363_additional.map | ||||||||||||
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Annotation | masked, sharpened cryo-EM map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map
File | emd_22363_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map
File | emd_22363_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Drosophila ORC (active state)
Entire | Name: Drosophila ORC (active state) |
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Components |
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-Supramolecule #1: Drosophila ORC (active state)
Supramolecule | Name: Drosophila ORC (active state) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Origin recognition complex subunit 4
Macromolecule | Name: Origin recognition complex subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 52.277109 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: SNAMPEADRE LVSIRRFLKE RLQRDYTTLR GYAKERSNVR LLLQRTAEMG ESNSLLLLGP RGSGKTTLIN SVLADLLPNK SFGENTLIV HLDGNLHTDD RVALKSITVQ MQLENAADGK VFGSFAENLA FLLQCLKAGG KHSKSVIFIL EEFDLFCAHH N QTLLYNLF ...String: SNAMPEADRE LVSIRRFLKE RLQRDYTTLR GYAKERSNVR LLLQRTAEMG ESNSLLLLGP RGSGKTTLIN SVLADLLPNK SFGENTLIV HLDGNLHTDD RVALKSITVQ MQLENAADGK VFGSFAENLA FLLQCLKAGG KHSKSVIFIL EEFDLFCAHH N QTLLYNLF DVSQSAQAPI CVLGVTCRLD VIELLEKRVK SRFSHRQVFL FPSLRRFEDY VDLCRDLLSL PTGNSLLLAA EK IYNLQNI QSGALYFSRN HFDPGEYGFS PRLRDAWNKQ ICKVLATQQA RSTLQALHDF DISEAYLKNF LFRLVAHLRP QSP HITAEK MAAVGSQFEG DDKIELLCGL SVLELCLIIA IKHHSQIYDR DSFNFEIIYA RFSKFAKVST TMQAVERSIV LKAF EHLRI AELIMPLTGG AGGGVGKVQK EFEMHKLALT YSQIHHCMQR YQALPTEVAQ WAQSSLI UniProtKB: Origin recognition complex subunit 4 |
-Macromolecule #2: Origin recognition complex subunit 5
Macromolecule | Name: Origin recognition complex subunit 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 52.175066 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MEAICSSLEP LFPCREAAIE TLGELIGDSS ETYPSAIYLF GHSGTGKTAL TRAFLKECGK RQNVRTAHLN AIECYTTKIM LEILLDSLA PDQGDALKVD NMLDFVEQLR RQAATRVEDQ GFLIAVDNAE RLRDMDANVL PVLLRLQELT NLNLCVILLS Q LPFEKFYN ...String: MEAICSSLEP LFPCREAAIE TLGELIGDSS ETYPSAIYLF GHSGTGKTAL TRAFLKECGK RQNVRTAHLN AIECYTTKIM LEILLDSLA PDQGDALKVD NMLDFVEQLR RQAATRVEDQ GFLIAVDNAE RLRDMDANVL PVLLRLQELT NLNLCVILLS Q LPFEKFYN KTGLSEIVCL HLAQYNKAET QRILGSDFQQ VRNQLLEQFA QDKKRLEICQ EAVTEDFYNN YLNLFLSVFY KA CRDVPEL QLTARKCLST YLEPVLDGTV DATDISRLWR HIAGPLRSAL TQIYMRIEKP AEEVEDFTAI EDQSVRKLAQ SLE LPYYAK FLLIAAFLAS HNAAKQDKRL FVKHHGKQRK RMQTVNARAK TTEKMSTTLG PKSFSIDRLL AIFYAILEEK VGLT CNLLS QISTLVHLNL LSFVSGEQNI MEGSARLQCT IGLEFVLQIG KVVGFNVRQY LCDFM UniProtKB: Origin recognition complex subunit 5 |
-Macromolecule #3: Origin recognition complex subunit 1
Macromolecule | Name: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 54.485633 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: SNAPRRSIHL SNIVEQRVFE DDEIISTPKR GRSKKTVQDN DEDYSPKKSV QKTPTRTRRS STTTKTATTP SKGITTATAT PMTPSQKMK KIRAGELSPS MQQRTDLPAK DSSKSELQLA REQLHVSVVP KSLPCREREF ENIYAFLEGK IQDQCGGCMY V SGVPGTGK ...String: SNAPRRSIHL SNIVEQRVFE DDEIISTPKR GRSKKTVQDN DEDYSPKKSV QKTPTRTRRS STTTKTATTP SKGITTATAT PMTPSQKMK KIRAGELSPS MQQRTDLPAK DSSKSELQLA REQLHVSVVP KSLPCREREF ENIYAFLEGK IQDQCGGCMY V SGVPGTGK TATVTGVIRT LQRMAKQNEL PAFEYLEING MRLTEPRQAY VQIYKQLTGK TVSWEQAHAL LEKRFTTPAP RR VTTVLLV DELDILCNRR QDVVYNLLDW PTKSAAKLVV VTIANTMDLP ERLLMGKVTS RLGLTRLTFQ PYSHKQLQEI VTA RLGGSE TFKGEAVQLV ARKVAAVSGD ARRALDICRR ATEIADTAAV KCVTMLHVQQ ALAEMIASAK VQAIRNCSRM EQIF LQAIA AEVTRTGVEE TTFMGVYQQV ETIAAFMGVT FPPPGRALRL CSKLGAERLI ISEHSRNDLF QKILLNVSAD DIHYA LRVE EMVN UniProtKB: Origin recognition complex subunit 1 |
-Macromolecule #4: Origin recognition complex subunit 2
Macromolecule | Name: Origin recognition complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 69.086445 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MSASNKGGYK TPRKENLMSI ENLTNSEEES EDLNTAMVGN AVESQPKVTS RRSTRRPSPT KKYQAYQKES NGKGQEERIV VNYVEMSDE RSSDAEDQEE EESIEESENA ARPAAKDLHL IQSEYNVAGT SMFGFNTPKK RDAMALAALN ATPCTPKTPK T PRLGVKTP ...String: MSASNKGGYK TPRKENLMSI ENLTNSEEES EDLNTAMVGN AVESQPKVTS RRSTRRPSPT KKYQAYQKES NGKGQEERIV VNYVEMSDE RSSDAEDQEE EESIEESENA ARPAAKDLHL IQSEYNVAGT SMFGFNTPKK RDAMALAALN ATPCTPKTPK T PRLGVKTP DTKRKKSMDQ PKTPAHVRTR VKKQIAKIVA DSDEDFSGDE SDFRPSDEES SSSSSSSDAG NSSDNDAADD EP KTPSRAR RAIVVPVLPK TPSAARLRQS ARAKKSNEFV PESDGYFHSH ASSKILTSDH TLDRLKNPRL AADRVFSLLS EIK TSAEHE GSINAIMEEY RSYFPKWMCI LNEGFNILLY GLGSKHQLLQ SFHREVLHKQ TVLVVNGFFP SLTIKDMLDS ITSD ILDAG ISPANPHEAV DMIEEEFALI PETHLFLIVH NLDGAMLRNV KAQAILSRLA RIPNIHLLAS IDHINTPLLW DQGKL CSFN FSWWDCTTML PYTNETAFEN SLLVQNSGEL ALSSMRSVFS SLTTNSRGIY MLIVKYQLKN KGNATYQGMP FRDLYS SCR EAFLVSSDLA LRAQLTEFLD HKLVKSKRSV DGSEQLTIPI DGALLQQFLE EQEKK UniProtKB: Origin recognition complex subunit 2 |
-Macromolecule #5: Origin recognition complex subunit 3
Macromolecule | Name: Origin recognition complex subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 82.364523 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDPTISVSKG CFVYKNGATR AGKKAASKRK RPAAESSSLL GKEVVQQPFY EEYRKAWNQI NDHIADLQHR SYARTLEQLV DFVVGQAER DTPDEVLPTA ALLTGINQPD HLSQFTALTQ RLHAQRAAMV CVLQSRDCAT LKAAVETLVF GLVEDNAEVE Q MEDEDEDE ...String: MDPTISVSKG CFVYKNGATR AGKKAASKRK RPAAESSSLL GKEVVQQPFY EEYRKAWNQI NDHIADLQHR SYARTLEQLV DFVVGQAER DTPDEVLPTA ALLTGINQPD HLSQFTALTQ RLHAQRAAMV CVLQSRDCAT LKAAVETLVF GLVEDNAEVE Q MEDEDEDE DGAERDRKRL RRSQCTMKQL KSWYTNNFDS EQKRRQLVVI LPDFECFNAS VLQDLILILS AHCGSLPFVL VL GVATAMT AVHGTLPYHV SSKIRLRVFQ TQAAPTGLNE VLDKVLLSPK YAFHLSGKTF KFLTHIFLYY DFSIHGFIQG FKY CLMEHF FGGNAFALCT DYSKALGRIK QLTHEDMETI RRLPSFRPYV EQINDCKRII AVLTDDDYLK KKLPQLLRDC LLHF LLFRC SLEFLTELVG DLPRCPLGKL RRELYVNCLN RAIISTPEYK ECLQMLSFLS KDEFVAKVNR ALERTEQFLV EEIAP LELG EACTAVLRPK LEAIRLAVDE VVKATMATIT TTSPNETRQA TDHLTPVASR QELKDQLLQR SKEDKMRHQL NTPTTQ FGR ALQKTLQLIE TQIVQDHLRA LQDAPPIHEL FVFSDIATVR RNIIGAPRAA LHTALNNPHF YMQCKCCELQ DQSLLVG TL PDLSVVYKLH LECGRMINLF DWLQAFRSVV SDSDHEEVAQ EQIDPQIQAR FTRAVAELQF LGYIKMSKRK TDHATRLT W UniProtKB: Origin recognition complex subunit 3 |
-Macromolecule #6: Origin recognition complex subunit 6
Macromolecule | Name: Origin recognition complex subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 29.284129 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MTTLIEQLIT KMGLREEPNV LEKTTELVRL LELRSTNVPL QINEYGKIVL CADLASCMIG IAFDKEQALK LSGLRKSQYL NNKRMFEKL LDLNKLASVN DICVQLGLNE VARKAEELMT LFKGVAATED MGTDTSHPQY ATMAVFQACR LLKKKVSKSK L MPFSNLRP ...String: MTTLIEQLIT KMGLREEPNV LEKTTELVRL LELRSTNVPL QINEYGKIVL CADLASCMIG IAFDKEQALK LSGLRKSQYL NNKRMFEKL LDLNKLASVN DICVQLGLNE VARKAEELMT LFKGVAATED MGTDTSHPQY ATMAVFQACR LLKKKVSKSK L MPFSNLRP SQFQLLEQQW ERMIAKHHKE SKVPSSTDME GKLKENQNEN IKGHEAKKAH KPPPEDYEIW KARMLAKAQA KL KELEASQ SHMDSQLLEA UniProtKB: Origin recognition complex subunit 6 |
-Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 3 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #8: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | The complex used for grid preparation was reconstituted with DNA. This structure was obtained from a subset of particles not bound to DNA. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |