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Yorodumi- PDB-6bc8: Crystal structure of Rev7-R124A/Rev3-RBM2 (residues 1988-2014) complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bc8 | ||||||||||||||||||||||||
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Title | Crystal structure of Rev7-R124A/Rev3-RBM2 (residues 1988-2014) complex | ||||||||||||||||||||||||
Components |
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Keywords | REPLICATION / DNA damage tolerance / translesion DNA synthesis | ||||||||||||||||||||||||
Function / homology | Function and homology information 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 / negative regulation of epithelial to mesenchymal transition ...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 / negative regulation of epithelial to mesenchymal transition / JUN kinase binding / 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 / actin filament organization / regulation of cell growth / double-strand break repair via homologous recombination / negative regulation of canonical Wnt signaling pathway / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / DNA-templated DNA replication / spindle / double-strand break repair / positive regulation of peptidyl-serine phosphorylation / site of double-strand break / chromosome / 4 iron, 4 sulfur cluster binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cell division / nucleotide binding / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||||||||||||||||||||
Authors | Rizzo, A.A. / Hao, B. / Li, Y. / Korzhnev, D.M. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Rev7 dimerization is important for assembly and function of the Rev1/Polζ translesion synthesis complex. Authors: Alessandro A Rizzo / Faye-Marie Vassel / Nimrat Chatterjee / Sanjay D'Souza / Yunfeng Li / Bing Hao / Michael T Hemann / Graham C Walker / Dmitry M Korzhnev / Abstract: The translesion synthesis (TLS) polymerases Polζ and Rev1 form a complex that enables replication of damaged DNA. The Rev7 subunit of Polζ, which is a multifaceted HORMA (Hop1, Rev7, Mad2) protein ...The translesion synthesis (TLS) polymerases Polζ and Rev1 form a complex that enables replication of damaged DNA. The Rev7 subunit of Polζ, which is a multifaceted HORMA (Hop1, Rev7, Mad2) protein with roles in TLS, DNA repair, and cell-cycle control, facilitates assembly of this complex by binding Rev1 and the catalytic subunit of Polζ, Rev3. Rev7 interacts with Rev3 by a mechanism conserved among HORMA proteins, whereby an open-to-closed transition locks the ligand underneath the "safety belt" loop. Dimerization of HORMA proteins promotes binding and release of this ligand, as exemplified by the Rev7 homolog, Mad2. Here, we investigate the dimerization of Rev7 when bound to the two Rev7-binding motifs (RBMs) in Rev3 by combining in vitro analyses of Rev7 structure and interactions with a functional assay in a Rev7 cell line. We demonstrate that Rev7 uses the conventional HORMA dimerization interface both to form a homodimer when tethered by the two RBMs in Rev3 and to heterodimerize with other HORMA domains, Mad2 and p31 Structurally, the Rev7 dimer can bind only one copy of Rev1, revealing an unexpected Rev1/Polζ architecture. In cells, mutation of the Rev7 dimer interface increases sensitivity to DNA damage. These results provide insights into the structure of the Rev1/Polζ TLS assembly and highlight the function of Rev7 homo- and heterodimerization. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bc8.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bc8.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/6bc8 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/6bc8 | HTTPS FTP |
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-Related structure data
Related structure data | 6bcdC 6bi7C 3abdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26101.236 Da / Num. of mol.: 1 / Mutation: R124A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L2, MAD2B, REV7 / Plasmid: pETDuet / Details (production host): MCS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UI95 | ||||
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#2: Protein/peptide | Mass: 3278.004 Da / Num. of mol.: 1 / Fragment: residues 1988-2014 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REV3L, POLZ, REV3 / Plasmid: pETDuet / Details (production host): MCS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60673, DNA-directed DNA polymerase | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: well solution containing 100 mM sodium acetate, 200 mM NaCl, 1.4 M ammonium sulfate was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4 |
-Data collection
Diffraction | Mean temperature: 77.15 K / Ambient temp details: stream of liquid nitrogen |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→116.27 Å / Num. obs: 31583 / % possible obs: 99.6 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.022 / Rrim(I) all: 0.067 / Net I/σ(I): 40.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ABD (Rev7 molecule only) Resolution: 1.68→116.27 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.099 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.99 Å2 / Biso mean: 47.572 Å2 / Biso min: 28.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→116.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.683→1.726 Å / Total num. of bins used: 20
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