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- PDB-6bcd: Crystal structure of Rev7-K44A/R124A/A135D in complex with Rev3-R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bcd | |||||||||||||||||||||||||||
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Title | Crystal structure of Rev7-K44A/R124A/A135D in complex with Rev3-RBM2 (residues 1988-2014) | |||||||||||||||||||||||||||
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Function / homology | ![]() somatic diversification of immunoglobulins involved in immune response / DNA damage response, signal transduction resulting in transcription / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||||||||||||||
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![]() | Rizzo, A.A. / Hao, B. / Li, Y. / Korzhnev, D.M. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bc8C ![]() 6bi7C ![]() 3abdS C: citing same article ( S: Starting model for refinement |
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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: 26087.143 Da / Num. of mol.: 1 / Mutation: K44A, R124A, A135D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.2 % |
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Crystal grow![]() | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: well solution containing 100 mM sodium citrate, 1.6 M ammonium sulfate, pH=5.25 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: 289.15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.43→116.55 Å / Num. obs: 51936 / % possible obs: 98.5 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.016 / Rrim(I) all: 0.048 / Net I/σ(I): 41.78 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3ABD (excluding Rev3 peptide) Resolution: 1.43→116.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 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: 121.08 Å2 / Biso mean: 29.8026 Å2 / Biso min: 15.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→116.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.467 Å / Total num. of bins used: 20
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