[English] 日本語
Yorodumi- EMDB-31030: Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31030 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information CDC6 association with the ORC:origin complex / RNA polymerase I upstream activating factor complex / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / maintenance of rDNA / global genome nucleotide-excision repair / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...CDC6 association with the ORC:origin complex / RNA polymerase I upstream activating factor complex / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / maintenance of rDNA / global genome nucleotide-excision repair / 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 / HDACs deacetylate histones / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / RMTs methylate histone arginines / Oxidative Stress Induced Senescence / mitotic DNA replication checkpoint signaling / prenyltransferase activity / silent mating-type cassette heterochromatin formation / isoprenoid biosynthetic process / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / Orc1 removal from chromatin / nucleolar large rRNA transcription by RNA polymerase I / DNA replication origin binding / Estrogen-dependent gene expression / rRNA transcription / nucleosome binding / intracellular copper ion homeostasis / DNA replication initiation / Ub-specific processing proteases / CENP-A containing nucleosome / nucleosomal DNA binding / aerobic respiration / heterochromatin formation / structural constituent of chromatin / nucleosome / 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 | Saccharomyces cerevisiae S288C (yeast) / Escherichia coli (E. coli) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Jiang H / Yu C / Liu CP / Han X / Yu Z / Xu RM | |||||||||
Funding support | China, 2 items
| |||||||||
Citation | Journal: To Be Published 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_31030.map.gz | 4.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31030-v30.xml emd-31030.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31030_fsc.xml | 6.8 KB | Display | FSC data file |
Images | emd_31030.png | 78.7 KB | ||
Others | emd_31030_half_map_1.map.gz emd_31030_half_map_2.map.gz | 8.7 MB 8.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31030 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31030 | HTTPS FTP |
-Validation report
Summary document | emd_31030_validation.pdf.gz | 497.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_31030_full_validation.pdf.gz | 497.2 KB | Display | |
Data in XML | emd_31030_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_31030_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31030 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31030 | HTTPS FTP |
-Related structure data
Related structure data | 7e9fMC 7e9cC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_31030.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_31030_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_31030_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |