+Open data
-Basic information
Entry | Database: PDB / ID: 8b9d | ||||||
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Title | Human replisome bound by Pol Alpha | ||||||
Components |
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Keywords | REPLICATION / human / priming / polymerase | ||||||
Function / homology | Function and homology information DNA primase AEP / positive regulation of DNA primase activity / cellular response to bleomycin / ribonucleotide binding / DNA secondary structure binding / Switching of origins to a post-replicative state / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Unwinding of DNA ...DNA primase AEP / positive regulation of DNA primase activity / cellular response to bleomycin / ribonucleotide binding / DNA secondary structure binding / Switching of origins to a post-replicative state / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Unwinding of DNA / DNA replication initiation / cell cycle phase transition / cellular response to cisplatin / DNA strand elongation involved in mitotic DNA replication / DNA/RNA hybrid binding / GINS complex / mitotic DNA replication preinitiation complex assembly / Telomere C-strand synthesis initiation / nuclear origin of replication recognition complex / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / mitotic DNA replication / alpha DNA polymerase:primase complex / cellular response to hydroxyurea / regulation of type I interferon production / anaphase-promoting complex binding / CMG complex / DNA replication checkpoint signaling / Removal of the Flap Intermediate / DNA primase activity / Polymerase switching on the C-strand of the telomere / MCM complex / regulation of phosphorylation / DNA replication preinitiation complex / lagging strand elongation / double-strand break repair via break-induced replication / mitotic DNA replication checkpoint signaling / replication fork protection complex / mitotic DNA replication initiation / DNA replication, synthesis of primer / mitotic intra-S DNA damage checkpoint signaling / positive regulation of double-strand break repair / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / inner cell mass cell proliferation / leading strand elongation / DNA synthesis involved in DNA repair / branching morphogenesis of an epithelial tube / G1/S-Specific Transcription / replication fork processing / cochlea development / DNA unwinding involved in DNA replication / positive regulation of double-strand break repair via homologous recombination / nuclear replication fork / DNA replication origin binding / Apoptotic cleavage of cellular proteins / activation of protein kinase activity / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / response to UV / cellular response to interleukin-4 / DNA helicase activity / ciliary basal body / DNA damage checkpoint signaling / Defective pyroptosis / helicase activity / Assembly of the pre-replicative complex / morphogenesis of an epithelium / lung development / regulation of circadian rhythm / DNA-templated DNA replication / nuclear matrix / nucleosome assembly / double-strand break repair via nonhomologous end joining / Orc1 removal from chromatin / protein import into nucleus / circadian rhythm / cellular response to xenobiotic stimulus / single-stranded DNA binding / mitotic cell cycle / site of double-strand break / nuclear envelope / 4 iron, 4 sulfur cluster binding / Processing of DNA double-strand break ends / histone binding / peptidyl-serine phosphorylation / DNA helicase / cell population proliferation / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / Ub-specific processing proteases / cell cycle / cell division / nucleotide binding / DNA repair Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Jones, M.L. / Yeeles, J.T.P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol Cell / Year: 2023 Title: How Pol α-primase is targeted to replisomes to prime eukaryotic DNA replication. Authors: Morgan L Jones / Valentina Aria / Yasemin Baris / Joseph T P Yeeles / Abstract: During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand ...During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand replication. How Pol α-primase is targeted to replication forks to prime DNA synthesis is not fully understood. Here, by determining cryoelectron microscopy (cryo-EM) structures of budding yeast and human replisomes containing Pol α-primase, we reveal a conserved mechanism for the coordination of priming by the replisome. Pol α-primase binds directly to the leading edge of the CMG (CDC45-MCM-GINS) replicative helicase via a complex interaction network. The non-catalytic PRIM2/Pri2 subunit forms two interfaces with CMG that are critical for in vitro DNA replication and yeast cell growth. These interactions position the primase catalytic subunit PRIM1/Pri1 directly above the exit channel for lagging-strand template single-stranded DNA (ssDNA), revealing why priming occurs efficiently only on the lagging-strand template and elucidating a mechanism for Pol α-primase to overcome competition from RPA to initiate primer synthesis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b9d.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8b9d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8b9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/8b9d ftp://data.pdbj.org/pub/pdb/validation_reports/b9/8b9d | HTTPS FTP |
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-Related structure data
Related structure data | 15341MC 8b9aC 8b9bC 8b9cC 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 |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA replication licensing factor ... , 6 types, 6 molecules 234567
#1: Protein | Mass: 102034.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49736, DNA helicase |
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#2: Protein | Mass: 91110.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25205, DNA helicase |
#3: Protein | Mass: 96684.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM4, CDC21 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33991, DNA helicase |
#4: Protein | Mass: 82406.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM5, CDC46 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33992, DNA helicase |
#5: Protein | Mass: 93010.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14566, DNA helicase |
#6: Protein | Mass: 81411.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM7, CDC47, MCM2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P33993, DNA helicase |
-DNA polymerase alpha ... , 2 types, 2 molecules AB
#7: 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 |
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#21: Protein | Mass: 170392.656 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 |
-Protein , 7 types, 9 molecules CKLPQOHJI
#8: Protein | Mass: 66016.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC45, CDC45L, CDC45L2, UNQ374/PRO710 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75419 |
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#13: Protein | Mass: 138903.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIMELESS, TIM, TIM1, TIMELESS1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UNS1 |
#14: Protein | Mass: 34600.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIPIN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BVW5 |
#17: Protein | Mass: 58890.918 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 |
#18: Protein | Mass: 155184.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLSPN / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HAW4 |
#19: Protein | Mass: 54242.598 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, DNA primase AEP |
#20: Protein | Mass: 129966.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDHD1, AND1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75717 |
-DNA replication complex GINS protein ... , 4 types, 4 molecules DEFG
#9: Protein | Mass: 23022.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS1, KIAA0186, PSF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14691 |
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#10: Protein | Mass: 21453.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS2, PSF2, CGI-122, DC5, HSPC037 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y248 |
#11: Protein | Mass: 24562.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS3, PSF3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BRX5 |
#12: Protein | Mass: 29983.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GINS4, SLD5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BRT9 |
-DNA chain , 2 types, 2 molecules MN
#15: DNA chain | Mass: 26092.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#16: DNA chain | Mass: 26402.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 10 molecules
#22: Chemical | #23: Chemical | #24: Chemical | ChemComp-ZN / |
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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 replisome bound by pol alpha, engaged on a fork DNA substrate with a 60 nucleotide lagging strand. Type: COMPLEX Entity ID: #19, #7, #21, #17, #1-#6, #8-#12, #20, #13-#16, #18 Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 37.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20_4459: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174696 / Symmetry type: POINT | ||||||||||||||||||||||||
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