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Yorodumi- EMDB-26346: Cryo-EM structure of human CST bound to DNA polymerase alpha-prim... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26346 | |||||||||
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Title | Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state | |||||||||
Map data | Human CST-Pol alpha/Primase bound to ssDNA in a recruitment state. | |||||||||
Sample |
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Keywords | Fill-in / Telomere / Replication / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information CST complex / positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / telomerase inhibitor activity / DNA replication initiation / telomere maintenance via telomere lengthening / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 ...CST complex / positive regulation of DNA primase activity / DNA primase AEP / ribonucleotide binding / telomerase inhibitor activity / DNA replication initiation / telomere maintenance via telomere lengthening / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / regulation of type I interferon production / Polymerase switching / telomere capping / alpha DNA polymerase:primase complex / Processive synthesis on the lagging strand / single-stranded telomeric DNA binding / DNA primase activity / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / primosome complex / G-rich strand telomeric DNA binding / DNA replication, synthesis of primer / lagging strand elongation / mitotic DNA replication initiation / bone marrow development / DNA strand elongation involved in DNA replication / intermediate filament cytoskeleton / hematopoietic stem cell proliferation / DNA synthesis involved in DNA repair / telomeric DNA binding / G1/S-Specific Transcription / leading strand elongation / DNA replication origin binding / negative regulation of telomere maintenance via telomerase / replicative senescence / Activation of the pre-replicative complex / DNA replication initiation / spleen development / regulation of G2/M transition of mitotic cell cycle / telomere maintenance / thymus development / positive regulation of DNA replication / Defective pyroptosis / multicellular organism growth / fibrillar center / double-strand break repair via nonhomologous end joining / nuclear matrix / protein import into nucleus / positive regulation of fibroblast proliferation / nuclear envelope / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / intracellular membrane-bounded organelle / DNA repair / nucleotide binding / DNA damage response / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Cai SW / Zinder JC / Svetlov V / Bush MW / Nudler E / Walz T / de Lange T | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Cryo-EM structure of the human CST-Polα/primase complex in a recruitment state. Authors: Sarah W Cai / John C Zinder / Vladimir Svetlov / Martin W Bush / Evgeny Nudler / Thomas Walz / Titia de Lange / Abstract: The CST-Polα/primase complex is essential for telomere maintenance and functions to counteract resection at double-strand breaks. We report a 4.6-Å resolution cryo-EM structure of human CST- ...The CST-Polα/primase complex is essential for telomere maintenance and functions to counteract resection at double-strand breaks. We report a 4.6-Å resolution cryo-EM structure of human CST-Polα/primase, captured prior to catalysis in a recruitment state stabilized by chemical cross-linking. Our structure reveals an evolutionarily conserved interaction between the C-terminal domain of the catalytic POLA1 subunit and an N-terminal expansion in metazoan CTC1. Cross-linking mass spectrometry and negative-stain EM analysis provide insight into CST binding by the flexible POLA1 N-terminus. Finally, Coats plus syndrome disease mutations previously characterized to disrupt formation of the CST-Polα/primase complex map to protein-protein interfaces observed in the recruitment state. Together, our results shed light on the architecture and stoichiometry of the metazoan fill-in machinery. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26346.map.gz | 95.9 MB | EMDB map data format | |
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Header (meta data) | emd-26346-v30.xml emd-26346.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26346_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_26346.png | 96.1 KB | ||
Filedesc metadata | emd-26346.cif.gz | 9.1 KB | ||
Others | emd_26346_half_map_1.map.gz emd_26346_half_map_2.map.gz | 80.9 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26346 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26346 | HTTPS FTP |
-Validation report
Summary document | emd_26346_validation.pdf.gz | 939 KB | Display | EMDB validaton report |
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Full document | emd_26346_full_validation.pdf.gz | 938.5 KB | Display | |
Data in XML | emd_26346_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_26346_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26346 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26346 | HTTPS FTP |
-Related structure data
Related structure data | 7u5cMC 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-11131 (Title: Single particle cryo-EM of the human CST•Polα/Primase (POLA1ΔN) complex in a recruitment state Data size: 869.0 Data #1: Motion corrected micrographs of CST-Pola/Primase deltaN complex in recruitment state [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26346.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human CST-Pol alpha/Primase bound to ssDNA in a recruitment state. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_26346_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26346_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in...
+Supramolecule #1: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in...
+Macromolecule #1: DNA primase small subunit
+Macromolecule #2: DNA primase large subunit
+Macromolecule #3: DNA polymerase alpha catalytic subunit
+Macromolecule #4: DNA polymerase alpha subunit B
+Macromolecule #5: CST complex subunit CTC1
+Macromolecule #6: CST complex subunit STN1
+Macromolecule #7: CST complex subunit TEN1
+Macromolecule #8: canonical telomeric DNA sequence
+Macromolecule #9: ZINC ION
+Macromolecule #10: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.075 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
Details | The sample was cross-linked with glutaraldehyde (GraFix) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |