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Open data
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Basic information
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Title | Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction | ||||||||||||
![]() | Open state of Yeast Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction | ||||||||||||
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![]() | DNA damage / DNA replication / DNA sliding clamp / REPLICATION / REPLICATION-DNA complex | ||||||||||||
Function / homology | ![]() meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / DNA clamp unloading / Gap-filling DNA repair synthesis and ligation in GG-NER / Ctf18 RFC-like complex / Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / DNA clamp unloading / Gap-filling DNA repair synthesis and ligation in GG-NER / Ctf18 RFC-like complex / Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / DNA clamp loader activity / telomere maintenance via recombination / 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 / recombinational repair / mitotic intra-S DNA damage checkpoint signaling / mitotic sister chromatid cohesion / leading strand elongation / protein kinase activator activity / mitotic G2 DNA damage checkpoint signaling / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / telomere maintenance / meiotic cell cycle / condensed nuclear chromosome / DNA damage checkpoint signaling / cellular response to ionizing radiation / nucleotide-excision repair / double-strand break repair via homologous recombination / DNA-templated DNA replication / double-strand break repair / site of double-strand break / double-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / DNA repair / chromatin binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||||||||
![]() | Castaneda JC / Schrecker M | ||||||||||||
Funding support | 3 items
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![]() | ![]() Title: Mechanisms of loading and release of the 9-1-1 checkpoint clamp. Authors: Juan C Castaneda / Marina Schrecker / Dirk Remus / Richard K Hite / ![]() Abstract: Single-stranded or double-stranded DNA junctions with recessed 5' ends serve as loading sites for the checkpoint clamp, 9-1-1, which mediates activation of the apical checkpoint kinase, ATR. However, ...Single-stranded or double-stranded DNA junctions with recessed 5' ends serve as loading sites for the checkpoint clamp, 9-1-1, which mediates activation of the apical checkpoint kinase, ATR. However, the basis for 9-1-1's recruitment to 5' junctions is unclear. Here, we present structures of the yeast checkpoint clamp loader, Rad24-replication factor C (RFC), in complex with 9-1-1 and a 5' junction and in a post-ATP-hydrolysis state. Unexpectedly, 9-1-1 adopts both closed and planar open states in the presence of Rad24-RFC and DNA. Moreover, Rad24-RFC associates with the DNA junction in the opposite orientation of processivity clamp loaders with Rad24 exclusively coordinating the double-stranded region. ATP hydrolysis stimulates conformational changes in Rad24-RFC, leading to disengagement of DNA-loaded 9-1-1. Together, these structures explain 9-1-1's recruitment to 5' junctions and reveal new principles of sliding clamp loading. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 108.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.5 KB 27.5 KB | Display Display | ![]() |
Images | ![]() | 208.8 KB | ||
Filedesc metadata | ![]() | 8.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 467.3 KB | Display | ![]() |
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Full document | ![]() | 466.8 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7st9MC ![]() 7stbC ![]() 7steC 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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Annotation | Open state of Yeast Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 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:9-1-1:DNA
+Supramolecule #1: Rad24-RFC:9-1-1:DNA
+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: DNA damage checkpoint control protein RAD17
+Macromolecule #7: DNA damage checkpoint protein 1
+Macromolecule #8: DNA damage checkpoint control protein MEC3
+Macromolecule #9: DNA (50-MER)
+Macromolecule #10: DNA (5'-D(P*CP*GP*CP*TP*CP*CP*TP*TP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP...
+Macromolecule #11: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: GLUTAMIC ACID
+Macromolecule #14: THREONINE
+Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #16: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL | ||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV |
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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: 66.0 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 |