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Yorodumi- PDB-2n1g: Structure of C-terminal domain of human polymerase Rev1 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n1g | ||||||
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Title | Structure of C-terminal domain of human polymerase Rev1 in complex with PolD3 RIR-motif | ||||||
Components |
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Keywords | TRANSFERASE / Rev1 / PolD3 | ||||||
Function / homology | Function and homology information delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / deoxycytidyl transferase activity / zeta DNA polymerase complex / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / nucleotide-excision repair, DNA gap filling / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / deoxycytidyl transferase activity / zeta DNA polymerase complex / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / nucleotide-excision repair, DNA gap filling / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / error-free translesion synthesis / DNA biosynthetic process / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / protein-macromolecule adaptor activity / DNA replication / damaged DNA binding / DNA-directed DNA polymerase activity / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | fewest violations, model1 | ||||||
Authors | Pustovalova, Y. / Korzhnev, D. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Pol zeta Suggests a Mechanism of Polymerase Exchange upon Rev1/Pol zeta-Dependent Translesion Synthesis. Authors: Pustovalova, Y. / Magalhaes, M.T. / D'Souza, S. / Rizzo, A.A. / Korza, G. / Walker, G.C. / Korzhnev, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n1g.cif.gz | 690.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n1g.ent.gz | 598.7 KB | Display | PDB format |
PDBx/mmJSON format | 2n1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/2n1g ftp://data.pdbj.org/pub/pdb/validation_reports/n1/2n1g | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10954.614 Da / Num. of mol.: 1 / Fragment: hRev1-CT, unp residues 1158-1251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein/peptide | Mass: 1779.135 Da / Num. of mol.: 1 / Fragment: unp residues 231-246 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0039, POLD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15054 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-100% 13C; U-100% 15N] Rev1-CT, 0.5-0.8 mM PolD3, 50 mM potassium phosphate, 100 mM sodium chloride, 2 mM DTT, 0.5 mM EDTA, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 7.0 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |