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- PDB-8uh7: Structure of T4 Bacteriophage clamp loader bound to the T4 clamp,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8uh7 | ||||||
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Title | Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog | ||||||
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![]() | REPLICATION/DNA / Clamp loader / T4 / AAA+ATPase / REPLICATION / REPLICATION-DNA complex | ||||||
Function / homology | ![]() Rad17 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication ...Rad17 RFC-like complex / DNA clamp loader activity / DNA replication factor C complex / Elg1 RFC-like complex / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gee, C.L. / Marcus, K. / Kelch, B.A. / Makino, D.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM. Authors: Kendra Marcus / Yongjian Huang / Subu Subramanian / Christine L Gee / Kent Gorday / Sam Ghaffari-Kashani / Xiao Ran Luo / Lisa Zheng / Michael O'Donnell / Sriram Subramaniam / John Kuriyan / ![]() ![]() Abstract: Clamp loaders are AAA+ ATPases that facilitate high-speed DNA replication. In eukaryotic and bacteriophage clamp loaders, ATP hydrolysis requires interactions between aspartate residues in one ...Clamp loaders are AAA+ ATPases that facilitate high-speed DNA replication. In eukaryotic and bacteriophage clamp loaders, ATP hydrolysis requires interactions between aspartate residues in one protomer, present in conserved 'DEAD-box' motifs, and arginine residues in adjacent protomers. We show that functional defects resulting from a DEAD-box mutation in the T4 bacteriophage clamp loader can be compensated by widely distributed single mutations in the ATPase domain. Using cryo-EM, we discovered an unsuspected inactive conformation of the clamp loader, in which DNA binding is blocked and the catalytic sites are disassembled. Mutations that restore function map to regions of conformational change upon activation, suggesting that these mutations may increase DNA affinity by altering the energetic balance between inactive and active states. Our results show that there are extensive opportunities for evolution to improve catalytic efficiency when an inactive intermediate is involved. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 453.2 KB | Display | ![]() |
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PDB format | ![]() | 363.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8uk9C ![]() 8unfC ![]() 8unhC 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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Unit cell |
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Components
-Sliding-clamp-loader ... , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 21391.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 36189.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 1 types, 3 molecules FGH
#3: Protein | Mass: 25162.592 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#4: DNA chain | Mass: 9172.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#5: DNA chain | Mass: 6136.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 42 molecules ![](data/chem/img/08T.gif)
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#6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-ADP / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.11 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9739 Å / Relative weight: 1 |
Reflection | Resolution: 2.628→49.649 Å / Num. obs: 55509 / % possible obs: 92.9 % / Redundancy: 6.3 % / CC1/2: 0.978 / Rmerge(I) obs: 0.325 / Rpim(I) all: 0.141 / Rrim(I) all: 0.355 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.628→2.922 Å / Num. unique obs: 2775 / CC1/2: 0.306 / Rpim(I) all: 0.865 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 2.628→49.649 Å
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Refine LS restraints |
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LS refinement shell |
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