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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22362 | |||||||||
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Title | Structure of Drosophila ORC bound to DNA | |||||||||
![]() | unsharpened cryo-EM map | |||||||||
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![]() | origin recognition complex / DNA replication initiation / REPLICATION / REPLICATION-DNA complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Schmidt JM / Bleichert F | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 80.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.2 KB 29.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.8 KB | Display | ![]() |
Images | ![]() | 118 KB | ||
Filedesc metadata | ![]() | 8.3 KB | ||
Others | ![]() ![]() ![]() | 66.4 MB 80.8 MB 80.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jk5MC ![]() 7jgrC ![]() 7jgsC ![]() 7jk2C ![]() 7jk3C ![]() 7jk4C ![]() 7jk6C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | unsharpened 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: sharpened, masked cryo-EM map, filtered by local resolution
File | emd_22362_additional.map | ||||||||||||
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Annotation | sharpened, masked cryo-EM map, filtered by local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map
File | emd_22362_half_map_1.map | ||||||||||||
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Annotation | half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map
File | emd_22362_half_map_2.map | ||||||||||||
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Annotation | half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Drosophila ORC bound to AT-rich DNA
+Supramolecule #1: Drosophila ORC bound to AT-rich DNA
+Macromolecule #1: Origin recognition complex subunit 2
+Macromolecule #2: Origin recognition complex subunit 3
+Macromolecule #3: Origin recognition complex subunit 4
+Macromolecule #4: Origin recognition complex subunit 5
+Macromolecule #5: Origin recognition complex subunit 6
+Macromolecule #6: Origin recognition complex subunit 1
+Macromolecule #7: DNA (32-MER)
+Macromolecule #8: DNA (32-MER)
+Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Model: UltrAuFoil / 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 | Recombinantly expressed and purified Drosophila ORC was mixed with DNA and the DNA-bound complex purified by size exclusion chromatography. |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |