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Yorodumi- PDB-8f5q: Crystal structure of human PCNA in complex with the PIP box of FBH1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f5q | ||||||
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Title | Crystal structure of human PCNA in complex with the PIP box of FBH1 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Complex | ||||||
Function / homology | Function and homology information negative regulation of chromatin binding / response to intra-S DNA damage checkpoint signaling / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / DNA 3'-5' helicase / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina ...negative regulation of chromatin binding / response to intra-S DNA damage checkpoint signaling / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / DNA 3'-5' helicase / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / MutLalpha complex binding / Polymerase switching / DNA translocase activity / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / replisome / DNA catabolic process / 3'-5' DNA helicase activity / SCF ubiquitin ligase complex / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / negative regulation of double-strand break repair via homologous recombination / G1/S-Specific Transcription / replication fork processing / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / isomerase activity / epithelial cell differentiation / positive regulation of DNA repair / DNA helicase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by POLI / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / single-stranded DNA binding / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / double-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / nuclear body / positive regulation of protein phosphorylation / DNA repair / centrosome / DNA damage response / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Liu, J. / Chaves-Arquero, B. / Wei, P. / Tencer, H. / Zhang, G. / Blanco, F. / Kutateladze, T. | ||||||
Funding support | 1items
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Citation | Journal: Structure / Year: 2023 Title: Molecular insight into the PCNA-binding mode of FBH1. Authors: Liu, J. / Chaves-Arquero, B. / Wei, P. / Tencer, A.H. / Ruiz-Albor, A. / Zhang, G. / Blanco, F.J. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f5q.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f5q.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 8f5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f5q ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f5q | HTTPS FTP |
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-Related structure data
Related structure data | 5iy4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28651.621 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004 #2: Protein/peptide | Mass: 1127.292 Da / Num. of mol.: 3 / Fragment: PIP box (UNP residues 56-64) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NFZ0, DNA helicase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride, 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.28 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.79 Å / Num. obs: 62010 / % possible obs: 98.28 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.04254 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.968 Å / Num. unique obs: 11431 / CC1/2: 0.567 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5IY4 Resolution: 1.9→41.79 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.79 Å
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Refine LS restraints |
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LS refinement shell |
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