+Open data
-Basic information
Entry | Database: PDB / ID: 7u19 | ||||||||||||
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Title | RFC:PCNA bound to nicked DNA | ||||||||||||
Components |
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Keywords | REPLICATION / sliding clamp / DNA replication&repair / AAA+ / clamp loader / BRCT domain | ||||||||||||
Function / homology | Function and homology information DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA replication factor C complex / Ctf18 RFC-like complex / meiotic mismatch repair / DNA clamp loader activity / Processive synthesis on the lagging strand / Removal of the Flap Intermediate ...DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / DNA replication factor C complex / Ctf18 RFC-like complex / meiotic mismatch repair / DNA clamp loader activity / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Polymerase switching / positive regulation of DNA metabolic process / SUMOylation of DNA replication proteins / maintenance of DNA trinucleotide repeats / PCNA complex / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / lagging strand elongation / postreplication repair / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / leading strand elongation / DNA polymerase processivity factor activity / error-free translesion synthesis / Gap-filling DNA repair synthesis and ligation in TC-NER / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA replication / translesion synthesis / positive regulation of DNA repair / replication fork / DNA damage checkpoint signaling / nucleotide-excision repair / DNA-templated DNA replication / mitotic cell cycle / chromosome, telomeric region / cell division / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Liu, X. / Gaubitz, C. / Pajak, J. / Kelch, B.A. | ||||||||||||
Funding support | United States, Switzerland, 3items
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Citation | Journal: Elife / Year: 2022 Title: A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA. Authors: Xingchen Liu / Christl Gaubitz / Joshua Pajak / Brian A Kelch / Abstract: Clamp loaders place circular sliding clamp proteins onto DNA so that clamp-binding partner proteins can synthesize, scan, and repair the genome. DNA with nicks or small single-stranded gaps are ...Clamp loaders place circular sliding clamp proteins onto DNA so that clamp-binding partner proteins can synthesize, scan, and repair the genome. DNA with nicks or small single-stranded gaps are common clamp-loading targets in DNA repair, yet these substrates would be sterically blocked given the known mechanism for binding of primer-template DNA. Here, we report the discovery of a second DNA binding site in the yeast clamp loader replication factor C (RFC) that aids in binding to nicked or gapped DNA. This DNA binding site is on the external surface and is only accessible in the open conformation of RFC. Initial DNA binding at this site thus provides access to the primary DNA binding site in the central chamber. Furthermore, we identify that this site can partially unwind DNA to create an extended single-stranded gap for DNA binding in RFC's central chamber and subsequent ATPase activation. Finally, we show that deletion of the BRCT domain, a major component of the external DNA binding site, results in defective yeast growth in the presence of DNA damage where nicked or gapped DNA intermediates occur. We propose that RFC's external DNA binding site acts to enhance DNA binding and clamp loading, particularly at DNA architectures typically found in DNA repair. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u19.cif.gz | 514.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u19.ent.gz | 409.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/7u19 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/7u19 | HTTPS FTP |
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-Related structure data
Related structure data | 26297MC 7u1aC 7u1pC C: citing same article (ref.) M: map data used to model this data |
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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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-Components
-Replication factor C subunit ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 95048.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC1, CDC44, YOR217W, YOR50-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38630 |
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#2: Protein | Mass: 36201.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC4, YOL094C, O0923 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40339 |
#3: Protein | Mass: 38254.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC3, YNL290W, N0533 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38629 |
#4: Protein | Mass: 39794.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC2, YJR068W, J1808 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40348 |
#5: Protein | Mass: 39993.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RFC5, YBR087W, YBR0810 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38251 |
-Protein , 1 types, 3 molecules FGH
#6: Protein | Mass: 29525.713 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: POL30, YBR088C, YBR0811 / Production host: Escherichia coli (E. coli) / References: UniProt: P15873 |
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-DNA chain , 3 types, 3 molecules IJK
#7: DNA chain | Mass: 6145.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#8: DNA chain | Mass: 10400.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#9: DNA chain | Mass: 3997.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 9 molecules
#10: Chemical | ChemComp-AGS / #11: Chemical | ChemComp-MG / #12: Chemical | ChemComp-ADP / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RFC bound to PCNA and DNA with a nick / Type: COMPLEX / Entity ID: #1-#9 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.367 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE |
Image recording | Electron dose: 48.6664 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119631 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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