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Yorodumi- PDB-7u5c: Cryo-EM structure of human CST bound to DNA polymerase alpha-prim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u5c | |||||||||
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Title | Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / 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 / DNA/RNA hybrid binding / telomere maintenance via telomere lengthening / 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 / DNA/RNA hybrid binding / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / regulation of type I interferon production / Processive synthesis on the lagging strand / DNA primase activity / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / lagging strand elongation / G-rich strand telomeric DNA binding / DNA replication, synthesis of primer / mitotic DNA replication initiation / telomere capping / bone marrow development / intermediate filament cytoskeleton / hematopoietic stem cell proliferation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / telomeric DNA binding / leading strand elongation / G1/S-Specific Transcription / 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 / nuclear matrix / double-strand break repair via nonhomologous end joining / protein import into nucleus / positive regulation of fibroblast proliferation / single-stranded DNA binding / nuclear envelope / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / intracellular membrane-bounded organelle / DNA repair / DNA damage response / chromatin binding / chromatin / nucleolus / protein kinase binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Cai, S.W. / Zinder, J.C. / Svetlov, V. / Bush, M.W. / Nudler, E. / Walz, T. / de Lange, T. | |||||||||
Funding support | United States, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u5c.cif.gz | 692.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u5c.ent.gz | 545.9 KB | Display | PDB format |
PDBx/mmJSON format | 7u5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/7u5c ftp://data.pdbj.org/pub/pdb/validation_reports/u5/7u5c | HTTPS FTP |
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-Related structure data
Related structure data | 26346MC M: map data used to model this data 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
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 49981.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 59092.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
-DNA polymerase alpha ... , 2 types, 2 molecules CD
#3: Protein | Mass: 129635.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLA1, POLA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P09884, DNA-directed DNA polymerase |
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#4: Protein | Mass: 66015.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLA2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14181 |
-CST complex subunit ... , 3 types, 3 molecules EFG
#5: Protein | Mass: 135050.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTC1, C17orf68 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q2NKJ3 |
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#6: Protein | Mass: 42172.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STN1, OBFC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H668 |
#7: Protein | Mass: 13872.013 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEN1, C17orf106 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86WV5 |
-DNA chain , 1 types, 1 molecules H
#8: DNA chain | Mass: 5682.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 2 types, 5 molecules
#9: Chemical | ChemComp-ZN / #10: Chemical | ChemComp-SF4 / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human CST bound to DNA polymerase alpha(POLA1 delta N)-primase in a recruitment state Type: COMPLEX Details: Sample was GraFix cross-linked with glutaraldehyde. Entity ID: #1-#8 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.5 MDa / Experimental value: NO |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.075 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was cross-linked with glutaraldehyde (GraFix) |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131850 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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