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Yorodumi- PDB-8thd: Structure of the Saccharomyces cerevisiae clamp unloader Elg1-RFC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8thd | ||||||||||||
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Title | Structure of the Saccharomyces cerevisiae clamp unloader Elg1-RFC bound to PCNA | ||||||||||||
Components |
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Keywords | REPLICATION / DNA replication / DNA sliding clamp / PCNA clamp / clamp loader/unloader / Elg1-RFC unloader | ||||||||||||
Function / homology | Function and homology information DNA clamp unloading / Gap-filling DNA repair synthesis and ligation in GG-NER / Ctf18 RFC-like complex / Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / DNA clamp loader activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 ...DNA clamp unloading / Gap-filling DNA repair synthesis and ligation in GG-NER / Ctf18 RFC-like complex / Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / DNA clamp loader activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / DNA replication checkpoint signaling / PCNA complex / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / sister chromatid cohesion / mitotic sister chromatid cohesion / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / mismatch repair / translesion synthesis / DNA damage checkpoint signaling / DNA-templated DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å | ||||||||||||
Authors | Zheng, F. / Yao, Y.N. / Georgescu, R. / O'Donnell, M.E. / Li, H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structure of the PCNA unloader Elg1-RFC. Authors: Fengwei Zheng / Nina Y Yao / Roxana E Georgescu / Huilin Li / Michael E O'Donnell / Abstract: During DNA replication, the proliferating cell nuclear antigen (PCNA) clamps are loaded onto primed sites for each Okazaki fragment synthesis by the AAA heteropentamer replication factor C (RFC). ...During DNA replication, the proliferating cell nuclear antigen (PCNA) clamps are loaded onto primed sites for each Okazaki fragment synthesis by the AAA heteropentamer replication factor C (RFC). PCNA encircling duplex DNA is quite stable and is removed from DNA by the dedicated clamp unloader Elg1-RFC. Here, we show the cryo-EM structure of Elg1-RFC in various states with PCNA. The structures reveal essential features of Elg1-RFC that explain how it is dedicated to PCNA unloading. Specifically, Elg1 contains two external loops that block opening of the Elg1-RFC complex for DNA binding, and an "Elg1 plug" domain that fills the central DNA binding chamber, thereby reinforcing the exclusive PCNA unloading activity of Elg1-RFC. Elg1-RFC was capable of unloading PCNA using non-hydrolyzable AMP-PNP. Both RFC and Elg1-RFC could remove PCNA from covalently closed circular DNA, indicating that PCNA unloading occurs by a mechanism that is distinct from PCNA loading. Implications for the PCNA unloading mechanism are discussed. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8thd.cif.gz | 515.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8thd.ent.gz | 412.2 KB | Display | PDB format |
PDBx/mmJSON format | 8thd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8thd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8thd_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8thd_validation.xml.gz | 80.1 KB | Display | |
Data in CIF | 8thd_validation.cif.gz | 116.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/8thd ftp://data.pdbj.org/pub/pdb/validation_reports/th/8thd | HTTPS FTP |
-Related structure data
Related structure data | 41254MC 8thbC 8thcC M: map data used to model this data C: citing same article (ref.) |
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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
-Protein , 2 types, 4 molecules AFGH
#1: Protein | Mass: 91391.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ELG1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4F7G7 |
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#6: Protein | Mass: 29102.203 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PCNA / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6B7JGY6 |
-Replication factor C subunit ... , 4 types, 4 molecules BCDE
#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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40339 |
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#3: Protein | Mass: 37841.051 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: Saccharomyces cerevisiae (brewer's yeast) / 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: Saccharomyces cerevisiae (brewer's yeast) / 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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38251 |
-Non-polymers , 3 types, 8 molecules
#7: Chemical | ChemComp-AGS / #8: Chemical | #9: Chemical | ChemComp-ADP / | |
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-Details
Has ligand of interest | N |
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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 |
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Source (natural) |
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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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173929 / Symmetry type: POINT | ||||||||||||||||||||||||
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