+Open data
-Basic information
Entry | Database: PDB / ID: 7l9p | ||||||
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Title | Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / REV7 / SHLD2 / SHLD3 / TRIP13 | ||||||
Function / homology | Function and homology information 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 / 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 ...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 / 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 / reciprocal meiotic recombination / oocyte maturation / female meiosis I / negative regulation of epithelial to mesenchymal transition / negative regulation of ubiquitin protein ligase activity / regulation of double-strand break repair via homologous recombination / oogenesis / positive regulation of double-strand break repair via nonhomologous end joining / mitotic spindle assembly checkpoint signaling / male meiosis I / telomere maintenance in response to DNA damage / spermatid development / negative regulation of double-strand break repair via homologous recombination / error-prone translesion synthesis / positive regulation of epithelial to mesenchymal transition / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / actin filament organization / male germ cell nucleus / regulation of cell growth / transcription coregulator activity / negative regulation of protein catabolic process / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / spindle / double-strand break repair / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / chromosome / site of double-strand break / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell division / DNA repair / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Xie, W. / Patel, D.J. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 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. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 7l9p.cif.gz | 545.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l9p.ent.gz | 435.6 KB | Display | PDB format |
PDBx/mmJSON format | 7l9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l9p_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7l9p_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7l9p_validation.xml.gz | 88.1 KB | Display | |
Data in CIF | 7l9p_validation.cif.gz | 130.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/7l9p ftp://data.pdbj.org/pub/pdb/validation_reports/l9/7l9p | HTTPS FTP |
-Related structure data
Related structure data | 23244MC 6ww9C 6wwaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: TRIP13, PCH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15645 #2: Protein | Mass: 24323.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: closed form / Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UI95 #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.) Homo sapiens (human) / Gene: SHLD2, FAM35A, RINN2, SHLD3, FLJ26957, RINN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86V20, UniProt: Q6ZNX1 #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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
-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 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 |
-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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