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- PDB-7thv: Structure of the yeast clamp loader (Replication Factor C RFC) bo... -
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Basic information
Entry | Database: PDB / ID: 7thv | |||||||||||||||
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Title | Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen PCNA) in an autoinhibited conformation | |||||||||||||||
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Function / homology | ![]() DNA clamp unloading / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Ctf18 RFC-like complex / Rad17 RFC-like complex / E3 ubiquitin ligases ubiquitinate target proteins / Elg1 RFC-like complex / Translesion Synthesis by POLH ...DNA clamp unloading / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Ctf18 RFC-like complex / Rad17 RFC-like complex / E3 ubiquitin ligases ubiquitinate target proteins / Elg1 RFC-like complex / Translesion Synthesis by POLH / DNA replication factor C complex / Polymerase switching / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / DNA clamp loader activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Gaubitz, C. / Liu, X. / Pajak, J. / Stone, N. / Hayes, J. / Demo, G. / Kelch, B.A. | |||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader. Authors: Christl Gaubitz / Xingchen Liu / Joshua Pajak / Nicholas P Stone / Janelle A Hayes / Gabriel Demo / Brian A Kelch / ![]() ![]() Abstract: Sliding clamps are ring-shaped protein complexes that are integral to the DNA replication machinery of all life. Sliding clamps are opened and installed onto DNA by clamp loader AAA+ ATPase complexes. ...Sliding clamps are ring-shaped protein complexes that are integral to the DNA replication machinery of all life. Sliding clamps are opened and installed onto DNA by clamp loader AAA+ ATPase complexes. However, how a clamp loader opens and closes the sliding clamp around DNA is still unknown. Here, we describe structures of the clamp loader Replication Factor C (RFC) bound to its cognate sliding clamp Proliferating Cell Nuclear Antigen (PCNA) en route to successful loading. RFC first binds to PCNA in a dynamic, closed conformation that blocks both ATPase activity and DNA binding. RFC then opens the PCNA ring through a large-scale 'crab-claw' expansion of both RFC and PCNA that explains how RFC prefers initial binding of PCNA over DNA. Next, the open RFC:PCNA complex binds DNA and interrogates the primer-template junction using a surprising base-flipping mechanism. Our structures indicate that initial PCNA opening and subsequent closure around DNA do not require ATP hydrolysis, but are driven by binding energy. ATP hydrolysis, which is necessary for RFC release, is triggered by interactions with both PCNA and DNA, explaining RFC's switch-like ATPase activity. Our work reveals how a AAA+ machine undergoes dramatic conformational changes for achieving binding preference and substrate remodeling. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 461.6 KB | Display | ![]() |
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PDB format | ![]() | 368.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 25614MC ![]() 7thjC ![]() 7ti8C ![]() 7tibC ![]() 7ticC ![]() 7tidC ![]() 7tkuC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() Gene: RFC1, CDC44, YOR217W, YOR50-7 / Production host: ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() Gene: RFC4, YOL094C, O0923 / Production host: ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 38254.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: RFC3, YNL290W, N0533 / Production host: ![]() ![]() ![]() |
#4: 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: ![]() ![]() ![]() |
#5: 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: ![]() ![]() ![]() |
-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.) ![]() ![]() ![]() Gene: POL30, YBR088C, YBR0811 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 3 types, 9 molecules ![](data/chem/img/AGS.gif)
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#7: Chemical | ChemComp-AGS / #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ADP / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: RFC bound to closed PCNA / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.336 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 6109 |
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Processing
Software | Name: PHENIX / Version: dev_3699: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | |||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60036 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1SXJ Accession code: 1SXJ / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||
Refine LS restraints |
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