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Open data
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Basic information
Entry | Database: PDB / ID: 7l9p | ||||||
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Title | Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex | ||||||
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![]() | NUCLEAR PROTEIN / REV7 / SHLD2 / SHLD3 / TRIP13 | ||||||
Function / homology | ![]() somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / meiotic recombination checkpoint signaling / zeta DNA polymerase complex / synaptonemal complex assembly / telomere maintenance in response to DNA damage / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / negative regulation of transcription regulatory region DNA binding / meiotic recombination checkpoint signaling / zeta DNA polymerase complex / synaptonemal complex assembly / telomere maintenance in response to DNA damage / positive regulation of isotype switching / positive regulation of extracellular matrix assembly / negative regulation of transcription by competitive promoter binding / negative regulation of cell-cell adhesion mediated by cadherin / JUN kinase binding / negative regulation of epithelial to mesenchymal transition / reciprocal meiotic recombination / female meiosis I / oocyte maturation / negative regulation of ubiquitin protein ligase activity / regulation of double-strand break repair via homologous recombination / oogenesis / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / male meiosis I / spermatid development / negative regulation of double-strand break repair via homologous recombination / male germ cell nucleus / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / transcription coregulator activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / negative regulation of protein catabolic process / regulation of cell growth / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / spindle / chromosome / positive regulation of peptidyl-serine phosphorylation / double-strand break repair / actin cytoskeleton / site of double-strand break / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell division / DNA repair / positive regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Xie, W. / Patel, D.J. | ||||||
![]() | ![]() Title: Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex. Authors: Wei Xie / Shengliu Wang / Juncheng Wang / M Jason de la Cruz / Guotai Xu / Maurizio Scaltriti / Dinshaw J Patel / ![]() Abstract: The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA ATPase TRIP13 remodels Shieldin to regulate DNA ...The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3-REV7 binary and fused SHLD2-SHLD3-REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2-SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2-SHLD3-REV7-TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 545.2 KB | Display | ![]() |
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PDB format | ![]() | 435.6 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 88.1 KB | Display | |
Data in CIF | ![]() | 130.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 23244MC ![]() 6ww9C ![]() 6wwaC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 48562.547 Da / Num. of mol.: 6 / Mutation: E253Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24323.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: closed form / Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 10678.139 Da / Num. of mol.: 2 Fragment: SHLD2 (UNP residues 5-19) + linker + SHLD3 (UNP residues 2-58) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-AGS / 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 |
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Sample preparation
Component | Name: SHLD2.3-REV7(4)-TRIP13(E253Q) complex with ATP-gamma-S Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.3 Details: 20 mM HEPES, pH 7.3, 300 mM NaCl, 5 mM MgCl2, 0.1 mM ATP-gamma-S, 1 mM DTT |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 1.5-second blot, blot force of 0 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -2500 nm / Nominal defocus min: -1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.075 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 40 |
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Processing
Software | Name: PHENIX / Version: 1.18_3855: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104023 / Symmetry type: POINT | ||||||||||||||||||||||||
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