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- EMDB-31029: Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucl... -
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Open data
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Basic information
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Title | Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome | |||||||||
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Function / homology | ![]() CDC6 association with the ORC:origin complex / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / maintenance of rDNA / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication ...CDC6 association with the ORC:origin complex / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / maintenance of rDNA / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / nuclear origin of replication recognition complex / HDACs deacetylate histones / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / mitotic DNA replication checkpoint signaling / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / positive regulation of transcription by RNA polymerase I / Orc1 removal from chromatin / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / DNA replication origin binding / rRNA transcription / Estrogen-dependent gene expression / DNA replication initiation / Ub-specific processing proteases / CENP-A containing nucleosome / heterochromatin organization / nucleosome binding / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Jiang H / Yu C / Liu CP / Han X / Yu Z / Xu RM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nucleosome binding relinquishes the association of the BAH domain of Orc1 with Sir1 Authors: Jiang H / Yu C / Liu CP / Han X / Yu Z / Xu RM | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.4 KB 23.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.8 KB | Display | ![]() |
Images | ![]() | 94.3 KB | ||
Others | ![]() ![]() | 25 MB 25 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 743.5 KB | Display | ![]() |
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Full document | ![]() | 743.1 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e9cMC ![]() 7e9fC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_31029_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31029_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : yeast Orc1 BAH domain in complex with 147-bp nucleosome
+Supramolecule #1: yeast Orc1 BAH domain in complex with 147-bp nucleosome
+Supramolecule #2: Histone
+Supramolecule #3: DNA
+Supramolecule #4: Origin recognition complex subunit 1
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A.2
+Macromolecule #4: Histone H2B.2
+Macromolecule #7: Origin recognition complex subunit 1
+Macromolecule #5: DNA (147-mer)
+Macromolecule #6: DNA (147-mer)
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |