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Open data
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Basic information
Entry | Database: PDB / ID: 8dqw | ||||||||||||
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Title | Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction | ||||||||||||
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![]() | REPLICATION/DNA / DNA damage checkpoint / REPLICATION-DNA complex | ||||||||||||
Function / homology | ![]() meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / 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 ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / 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 / telomere maintenance via recombination / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / reciprocal meiotic recombination / recombinational repair / sister chromatid cohesion / mitotic intra-S DNA damage checkpoint signaling / mitotic sister chromatid cohesion / leading strand elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / 3'-5' exonuclease activity / telomere maintenance / meiotic cell cycle / DNA damage checkpoint signaling / cellular response to ionizing radiation / nucleotide-excision repair / double-strand break repair via homologous recombination / DNA-templated DNA replication / double-strand break repair / site of double-strand break / double-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / cell cycle / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||||||||
![]() | Schrecker, M. / Hite, R.K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Multistep loading of a DNA sliding clamp onto DNA by replication factor C. Authors: Marina Schrecker / Juan C Castaneda / Sujan Devbhandari / Charanya Kumar / Dirk Remus / Richard K Hite / ![]() Abstract: The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader ...The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader replication factor C (RFC), which acts at single-stranded (ss)/double-stranded DNA (dsDNA) junctions harboring a recessed 3' end (3' ss/dsDNA junctions) and at DNA nicks. To illuminate the loading mechanism we have investigated the structure of RFC:PCNA bound to ATPγS and 3' ss/dsDNA junctions or nicked DNA using cryogenic electron microscopy. Unexpectedly, we observe open and closed PCNA conformations in the RFC:PCNA:DNA complex, revealing that PCNA can adopt an open, planar conformation that allows direct insertion of dsDNA, and raising the question of whether PCNA ring closure is mechanistically coupled to ATP hydrolysis. By resolving multiple DNA-bound states of RFC:PCNA we observe that partial melting facilitates lateral insertion into the central channel formed by RFC:PCNA. We also resolve the Rfc1 N-terminal domain and demonstrate that its single BRCT domain participates in coordinating DNA prior to insertion into the central RFC channel, which promotes PCNA loading on the lagging strand of replication forks in vitro. Combined, our data suggest a comprehensive and fundamentally revised model for the RFC-catalyzed loading of PCNA onto DNA. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 901.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 86.6 KB | Display | |
Data in CIF | ![]() | 132.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27662MC ![]() 8dqxC ![]() 8dqzC ![]() 8dr0C ![]() 8dr1C ![]() 8dr3C ![]() 8dr4C ![]() 8dr5C ![]() 8dr6C ![]() 8dr7C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Replication factor C subunit ... , 4 types, 4 molecules BCDE
#1: Protein | Mass: 36201.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RFC4, YOL094C, O0923 / Production host: ![]() ![]() |
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#2: Protein | Mass: 38254.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RFC3, YNL290W, N0533 / Production host: ![]() ![]() |
#3: Protein | Mass: 39794.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RFC2, YJR068W, J1808 / Production host: ![]() ![]() |
#4: Protein | Mass: 39993.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RFC5, YBR087W, YBR0810 / Production host: ![]() ![]() |
-DNA damage checkpoint control protein ... , 2 types, 2 molecules FH
#5: Protein | Mass: 45637.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RAD17, GI527_G0005737 / Production host: ![]() ![]() |
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#7: Protein | Mass: 53207.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MEC3, PIP3, PSO9, YLR288C, L8003.15 / Production host: ![]() ![]() |
-Protein , 2 types, 2 molecules GA
#6: Protein | Mass: 73850.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DDC1, GI527_G0005854 / Production host: ![]() ![]() |
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#8: Protein | Mass: 80096.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RAD24, GI527_G0001991 / Production host: ![]() ![]() |
-DNA chain , 2 types, 2 molecules JI
#9: DNA chain | Mass: 21507.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#10: DNA chain | Mass: 5972.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 438 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | ChemComp-MG / #12: Chemical | ChemComp-AGS / #13: Chemical | ChemComp-GDP / | #14: Water | ChemComp-HOH / | |
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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 |
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Sample preparation
Component | Name: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction Type: COMPLEX / Entity ID: #1, #3-#10 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: GRAPHENE OXIDE / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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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 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 938420 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7ST9 Accession code: 7ST9 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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