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Open data
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Basic information
Entry | Database: PDB / ID: 6wwa | ||||||
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Title | Crystal structure of human SHLD2-SHLD3-REV7 complex | ||||||
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![]() | NUCLEAR PROTEIN / REV7 / SHLD2 / 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 / regulation of double-strand break repair via homologous recombination / 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 / actin cytoskeleton / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 376.9 KB | Display | ![]() |
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PDB format | ![]() | 300 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
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Full document | ![]() | 489 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ww9C ![]() 7l9pC ![]() 3abdS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 24323.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 10678.139 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: 6.69 Å3/Da / Density % sol: 81.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1 M Na acetate pH 5.6, 1.5 M Na formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 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: 3.8→40 Å / Num. obs: 30856 / % possible obs: 99.74 % / Redundancy: 35.8 % / Biso Wilson estimate: 153.27 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.4031 / Rpim(I) all: 0.06797 / Rrim(I) all: 0.4089 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.8→3.936 Å / Rmerge(I) obs: 4.971 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 3027 / CC1/2: 0.472 / CC star: 0.801 / Rpim(I) all: 0.8316 / Rrim(I) all: 5.04 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ABD Resolution: 3.8→39.66 Å / SU ML: 0.5072 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5099 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: 189.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→39.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 109.905339802 Å / Origin y: 14.6069753103 Å / Origin z: 133.372128478 Å
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Refinement TLS group | Selection details: all |