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Yorodumi- EMDB-14527: Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 che... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14527 | |||||||||
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Title | Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp | |||||||||
Map data | Map | |||||||||
Sample |
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Function / homology | Function and homology information meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / response to organophosphorus / DNA clamp loader activity / positive regulation of DNA-directed DNA polymerase activity ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / response to organophosphorus / DNA clamp loader activity / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / Polymerase switching on the C-strand of the telomere / regulation of phosphorylation / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / DNA strand elongation involved in DNA replication / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA synthesis involved in DNA repair / negative regulation of DNA replication / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / ATP-dependent activity, acting on DNA / Activation of ATR in response to replication stress / response to UV / 3'-5' exonuclease activity / substantia nigra development / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / DNA damage checkpoint signaling / cellular response to ionizing radiation / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / SH3 domain binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / histone deacetylase binding / intrinsic apoptotic signaling pathway in response to DNA damage / site of double-strand break / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / DNA repair / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / nucleolus / protein kinase binding / enzyme binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
Authors | Day M / Oliver AW / Pearl LH | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction. Authors: Matthew Day / Antony W Oliver / Laurence H Pearl / Abstract: The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or ...The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5'-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5' DNA end and fixes the orientation of 9-1-1 on the ssDNA. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14527.map.gz | 87.6 MB | EMDB map data format | |
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Header (meta data) | emd-14527-v30.xml emd-14527.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14527_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_14527.png | 113.7 KB | ||
Others | emd_14527_half_map_1.map.gz emd_14527_half_map_2.map.gz | 77.4 MB 77.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14527 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14527 | HTTPS FTP |
-Related structure data
Related structure data | 7z6hMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11062 (Title: Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction Data size: 4.4 TB Data #1: unaligned multiframe EER movies for human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14527.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map 1
File | emd_14527_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_14527_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
+Supramolecule #1: DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
+Macromolecule #1: Cell cycle checkpoint control protein RAD9A
+Macromolecule #2: Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17
+Macromolecule #3: Checkpoint protein HUS1
+Macromolecule #4: Replication factor C subunit 4
+Macromolecule #5: Replication factor C subunit 3
+Macromolecule #6: Replication factor C subunit 2
+Macromolecule #7: Replication factor C subunit 5
+Macromolecule #8: Hairpin DNA
+Macromolecule #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.21 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 34.9 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |