[English] 日本語
Yorodumi- EMDB-17200: Cryo-EM density map of the C. elegans complex CMG helicase/TIM-1/... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17200 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM density map of the C. elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA (Multi-body Refinement GINS/CDC-45/DNSN-1 N-terminus) | |||||||||
Map data | Cryo-EM density map of the C. elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA (Multi-body Refinement GINS/CDC-45/DNSN-1 N-terminus) | |||||||||
Sample |
| |||||||||
Keywords | Replisome / DONSON / DNA replication / Initiation / REPLICATION | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Jenkyn-Bedford M / Yeeles JTP | |||||||||
Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: Science / Year: 2023 Title: DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in . Authors: Yisui Xia / Remi Sonneville / Michael Jenkyn-Bedford / Liqin Ji / Constance Alabert / Ye Hong / Joseph T P Yeeles / Karim P M Labib / Abstract: Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that ...Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that are not present in yeast. In this work, we show that DNSN-1, the ortholog of human DONSON, functions during helicase assembly in a complex with MUS-101/TOPBP1. DNSN-1 is required to recruit the GINS complex to chromatin, and a cryo-electron microscopy structure indicates that DNSN-1 positions GINS on the MCM-2-7 helicase motor (comprising the six MCM-2 to MCM-7 proteins), by direct binding of DNSN-1 to GINS and MCM-3, using interfaces that we show are important for initiation and essential for viability. These findings identify DNSN-1 as a missing link in our understanding of DNA replication initiation, suggesting that initiation defects underlie the human disease syndrome that results from DONSON mutations. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17200.map.gz | 69.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17200-v30.xml emd-17200.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_17200.png | 90.5 KB | ||
Filedesc metadata | emd-17200.cif.gz | 4.4 KB | ||
Others | emd_17200_half_map_1.map.gz emd_17200_half_map_2.map.gz | 78.9 MB 78.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17200 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17200 | HTTPS FTP |
-Validation report
Summary document | emd_17200_validation.pdf.gz | 686.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_17200_full_validation.pdf.gz | 685.7 KB | Display | |
Data in XML | emd_17200_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_17200_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17200 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17200 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_17200.map.gz / Format: CCP4 / Size: 120.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM density map of the C. elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA (Multi-body Refinement GINS/CDC-45/DNSN-1 N-terminus) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.295 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half-map 1. Cryo-EM density map of the C....
File | emd_17200_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map 1. Cryo-EM density map of the C. elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA (Multi-body Refinement GINS/CDC-45/DNSN-1 N-terminus) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map 2. Cryo-EM density map of the C....
File | emd_17200_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map 2. Cryo-EM density map of the C. elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA (Multi-body Refinement GINS/CDC-45/DNSN-1 N-terminus) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : In vitro reconstituted complex of Caenorhabditis elegans CMG heli...
Entire | Name: In vitro reconstituted complex of Caenorhabditis elegans CMG helicase bound by TIM-1/TIPN-1 and a homodimer of DNSN-1, on a synthetic forked DNA substrate |
---|---|
Components |
|
-Supramolecule #1: In vitro reconstituted complex of Caenorhabditis elegans CMG heli...
Supramolecule | Name: In vitro reconstituted complex of Caenorhabditis elegans CMG helicase bound by TIM-1/TIPN-1 and a homodimer of DNSN-1, on a synthetic forked DNA substrate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16 Details: All Caenorhabditis elegans proteins recombinantly expressed in either Saccharomyces cerevisiae (CMG helicase, TIM-1/TIPN-1) or Escherichia coli Rosetta (DE3) Competent cells (DNSN-1) |
---|---|
Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Details: PELCO easiGlow. 15 mA |
Vitrification | Cryogen name: ETHANE / Details: Manual plunger. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 10825 / Average exposure time: 1.7 sec. / Average electron dose: 40.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |