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- EMDB-25121: Cryo-EM 3D map of the yeast Rad24-RFC loader bound to DNA and the... -
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Open data
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Basic information
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Title | Cryo-EM 3D map of the yeast Rad24-RFC loader bound to DNA and the closed 9-1-1 clamp | ||||||||||||
![]() | Cryo-EM map of the yeast Rad24-RFC loader bound to the 911 clamp and DNA in a closed state | ||||||||||||
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![]() | DNA damage repair / Rad24-RFC / 9-1-1 clamp / DNA clamp / alternative clamp loader / DNA damage signaling / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | ![]() checkpoint clamp complex / DNA clamp unloading / Gap-filling DNA repair synthesis and ligation in GG-NER / Rad17 RFC-like complex / Ctf18 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / nuclease activity ...checkpoint clamp complex / DNA clamp unloading / Gap-filling DNA repair synthesis and ligation in GG-NER / Rad17 RFC-like complex / Ctf18 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / nuclease activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / leading strand elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / mismatch repair / DNA damage checkpoint signaling / nucleotide-excision repair / DNA-templated DNA replication / double-strand break repair / double-stranded DNA binding / damaged DNA binding / DNA repair / chromatin binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others) / ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | ||||||||||||
![]() | Zheng F / Georgescu R | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp. Authors: Fengwei Zheng / Roxana E Georgescu / Nina Y Yao / Michael E O'Donnell / Huilin Li / ![]() Abstract: The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in ...The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3'-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5'-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC-DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5'-DNA on its surface, not inside the loader, and threads the 3' ssDNA overhang into the 9-1-1 clamp from above the ring. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.4 KB 25.4 KB | Display Display | ![]() |
Images | ![]() | 86 KB | ||
Filedesc metadata | ![]() | 8.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 524 KB | Display | ![]() |
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Full document | ![]() | 523.5 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sgzMC ![]() 7sh2C C: citing same article ( M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||
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Annotation | Cryo-EM map of the yeast Rad24-RFC loader bound to the 911 clamp and DNA in a closed state | ||||||||||||||||||||
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
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Sample components
+Entire : Rad24-RFC-911 clamp-DNA
+Supramolecule #1: Rad24-RFC-911 clamp-DNA
+Supramolecule #2: dsDNA
+Supramolecule #3: Proteins
+Macromolecule #1: Checkpoint protein RAD24
+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: Mitosis Entry Checkpoint protein MEC3
+Macromolecule #7: DNA damage checkpoint control protein RAD17
+Macromolecule #8: DNA Damage Checkpoint protein DDC1
+Macromolecule #9: Watson strand
+Macromolecule #10: Crick strand
+Macromolecule #11: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: PHOSPHATE 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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 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 |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147415 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |