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Open data
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Basic information
Entry | Database: PDB / ID: 6ww9 | ||||||
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Title | Crystal structure of human REV7(R124A)-SHLD3(35-58) complex | ||||||
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![]() | NUCLEAR PROTEIN / REV7 / SHLD3 | ||||||
Function / homology | ![]() somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / 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 ...somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / telomere maintenance in response to DNA damage / negative regulation of transcription regulatory region DNA binding / zeta DNA polymerase complex / 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 / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair via nonhomologous end joining / 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 / regulation of cell growth / actin filament organization / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / chromosome / site of double-strand break / RNA polymerase II-specific DNA-binding transcription factor binding / cell division / DNA repair / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | 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
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 120.3 KB | Display | ![]() |
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PDB format | ![]() | 76.6 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 454 KB | Display | ![]() |
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Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wwaC ![]() 7l9pC ![]() 3abdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 24237.232 Da / Num. of mol.: 2 / Mutation: R124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 4094.845 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M ammonium acetate, 0.1 M Na citrate pH 5.6, 30% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.04 Å / Num. obs: 18113 / % possible obs: 97.75 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.8 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1652 / Rpim(I) all: 0.08723 / Rrim(I) all: 0.1884 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 2.7→2.796 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.319 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1755 / CC1/2: 0.453 / CC star: 0.79 / Rpim(I) all: 0.6845 / Rrim(I) all: 1.497 / % possible all: 99.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ABD Resolution: 2.7→29.04 Å / SU ML: 0.3107 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6071 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.04 Å
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LS refinement shell |
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