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Yorodumi- EMDB-25872: Cryo-EM 3D map of the S. cerevisiae clamp-clamp loader complex PC... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25872 | ||||||||||||
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Title | Cryo-EM 3D map of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end | ||||||||||||
Map data | 3D cryoEM map of yeast RFC-PCNA complexed with one 5'-recessed and one 3'-recessed dsDNA | ||||||||||||
Sample |
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Function / homology | Function and homology information DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA replication factor C complex / Ctf18 RFC-like complex / meiotic mismatch repair / DNA clamp loader activity / Processive synthesis on the lagging strand / Removal of the Flap Intermediate ...DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA replication factor C complex / Ctf18 RFC-like complex / meiotic mismatch repair / DNA clamp loader activity / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / PCNA complex / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / lagging strand elongation / postreplication repair / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / leading strand elongation / DNA polymerase processivity factor activity / error-free translesion synthesis / Gap-filling DNA repair synthesis and ligation in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / DNA damage checkpoint signaling / nucleotide-excision repair / DNA-templated DNA replication / mitotic cell cycle / chromosome, telomeric region / cell division / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others) / Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | ||||||||||||
Authors | Zheng F / Georgescu R / Yao YN / O'Donnell ME / Li H | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Elife / Year: 2022 Title: Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. Authors: Fengwei Zheng / Roxana Georgescu / Nina Y Yao / Huilin Li / Michael E O'Donnell / Abstract: RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during ...RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a second DNA binding site in RFC that binds a 5' duplex. This 5' DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3' and 5' ends are present at a ssDNA gap, we propose that the 5' site facilitates RFC's PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5' DNA binding domain of Rfc1. We further observe that a 5' end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5'-DNA site in lagging strand DNA synthesis. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25872.map.gz | 123.3 MB | EMDB map data format | |
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Header (meta data) | emd-25872-v30.xml emd-25872.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
Images | emd_25872.png | 80.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25872 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25872 | HTTPS FTP |
-Related structure data
Related structure data | 7tfhMC 7tfiC 7tfjC 7tfkC 7tflC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25872.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 3D cryoEM map of yeast RFC-PCNA complexed with one 5'-recessed and one 3'-recessed dsDNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : RFC-PCNA-DNA1-DNA2
+Supramolecule #1: RFC-PCNA-DNA1-DNA2
+Supramolecule #2: dsDNA
+Supramolecule #3: Proteins
+Macromolecule #1: Replication factor C subunit 1
+Macromolecule #2: Replication factor C subunit 4
+Macromolecule #3: Replication factor C subunit 3
+Macromolecule #4: Replication factor C subunit 2
+Macromolecule #5: Replication factor C subunit 5
+Macromolecule #6: Proliferating cell nuclear antigen
+Macromolecule #7: Template strand
+Macromolecule #8: Primer strand
+Macromolecule #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.3 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 432904 |