- EMDB-2789: Cryo-EM map of the Timeless-Tipin-RPA Complex -
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Basic information
Entry
Database: EMDB / ID: EMD-2789
Title
Cryo-EM map of the Timeless-Tipin-RPA Complex
Map data
Reconstruction of the Timless-Tipin-RPA complex
Sample
Sample: Timeless-Tipin-RPA complex
Protein or peptide: Timeless
Protein or peptide: Timeless-interacting protein
Protein or peptide: Replication protein A 70
Protein or peptide: Replication protein A 32
Protein or peptide: Replication protein A 14
Keywords
Timeless / Tipin / Replication protein A / RPA / DNA replication
Function / homology
Function and homology information
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Activation of ATR in response to replication stress / Removal of the Flap Intermediate / PCNA-Dependent Long Patch Base Excision Repair / Removal of the Flap Intermediate from the C-strand / Activation of the pre-replicative complex / : / Presynaptic phase of homologous DNA pairing and strand exchange / Regulation of HSF1-mediated heat shock response ...Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Activation of ATR in response to replication stress / Removal of the Flap Intermediate / PCNA-Dependent Long Patch Base Excision Repair / Removal of the Flap Intermediate from the C-strand / Activation of the pre-replicative complex / : / Presynaptic phase of homologous DNA pairing and strand exchange / Regulation of HSF1-mediated heat shock response / SUMOylation of DNA damage response and repair proteins / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / HDR through Single Strand Annealing (SSA) / Translesion synthesis by REV1 / Translesion synthesis by POLK / cellular response to bleomycin / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Translesion Synthesis by POLH / Termination of translesion DNA synthesis / Dual Incision in GG-NER / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein localization to chromosome / replication fork arrest / Processing of DNA double-strand break ends / DNA replication factor A complex / cell cycle phase transition / cellular response to cisplatin / : / cellular response to hydroxyurea / lateral element / Regulation of TP53 Activity through Phosphorylation / DNA replication checkpoint signaling / regulation of DNA damage checkpoint / single-stranded telomeric DNA binding / positive regulation of circadian rhythm / G-rich strand telomeric DNA binding / replication fork protection complex / mitotic intra-S DNA damage checkpoint signaling / positive regulation of double-strand break repair / branching involved in ureteric bud morphogenesis / regulation of double-strand break repair via homologous recombination / condensed chromosome / branching morphogenesis of an epithelial tube / DNA unwinding involved in DNA replication / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / site of DNA damage / hemopoiesis / telomere maintenance via telomerase / condensed nuclear chromosome / positive regulation of double-strand break repair via homologous recombination / chromosome organization / meiotic cell cycle / mismatch repair / male germ cell nucleus / response to UV / homeostasis of number of cells within a tissue / telomere maintenance / lung development / DNA damage checkpoint signaling / kidney development / morphogenesis of an epithelium / regulation of circadian rhythm / nucleotide-excision repair / double-strand break repair via homologous recombination / circadian rhythm / base-excision repair / PML body / site of double-strand break / single-stranded DNA binding / regulation of cell population proliferation / chromosome, telomeric region / protein phosphatase binding / DNA replication / in utero embryonic development / damaged DNA binding / nuclear body / cell division / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / DNA damage response / ubiquitin protein ligase binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function
Replication factor A protein 2 / Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor A protein 3 / Timeless, C-terminal / Timeless PAB domain / Replication factor A protein-like ...Replication factor A protein 2 / Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor A protein 3 / Timeless, C-terminal / Timeless PAB domain / Replication factor A protein-like / Replication factor-A protein 1, N-terminal domain / Chromosome segregation in meiosis protein 3 / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Replication factor A protein 1 / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / Timeless, N-terminal / Timeless, N-terminal / Timeless protein / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
Replication protein A 32 kDa subunit / Replication protein A 70 kDa DNA-binding subunit / TIMELESS-interacting protein / Replication protein A 14 kDa subunit / Protein timeless homolog Similarity search - Component
Biological species
Mus musculus (house mouse)
Method
single particle reconstruction / cryo EM / Resolution: 17.0 Å
Journal: Nucleic Acids Res / Year: 2014 Title: Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex. Authors: Justine Witosch / Eva Wolf / Naoko Mizuno / Abstract: The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks ...The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork.
History
Deposition
Oct 2, 2014
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Header (metadata) release
Nov 12, 2014
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Map release
Nov 12, 2014
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Update
Nov 19, 2014
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Current status
Nov 19, 2014
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 5 seconds with force 2, before plunging
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Electron microscopy
Microscope
FEI TECNAI F20
Alignment procedure
Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
Date
Oct 26, 2012
Image recording
Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 673 / Average electron dose: 20 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
The initial model was obtained using RCT. The refinement process was carried out using SPARX.
CTF correction
Details: Phases of individual images were flipped
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: SPARX / Details: The amplitude was corrected. / Number images used: 39679
Final two d classification
Number classes: 74
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