[English] 日本語
Yorodumi- EMDB-42399: Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding C... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42399 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | active / DNA-bound / REPLICATION | |||||||||
Function / homology | Function and homology information Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / DNA clamp loader activity / 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 replication factor C complex / Elg1 RFC-like complex / DNA clamp loader activity / 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 | Tequatrovirus T4 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Huang Y / Marcus K / Subramanian S / Gee LC / Gorday K / Ghaffari-Kashani S / Luo X / Zhang L / O'Donnell M / Kuriyan J | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2024 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_42399.map.gz | 15.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-42399-v30.xml emd-42399.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
Images | emd_42399.png | 161.7 KB | ||
Filedesc metadata | emd-42399.cif.gz | 6.9 KB | ||
Others | emd_42399_half_map_1.map.gz emd_42399_half_map_2.map.gz | 28.4 MB 28.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42399 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42399 | HTTPS FTP |
-Related structure data
Related structure data | 8unfMC 8uh7C 8uk9C 8unhC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_42399.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_42399_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_42399_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA (gp44+gp...
+Supramolecule #1: T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA (gp44+gp...
+Supramolecule #2: T4 Bacteriophage Sliding Clamp (gp45)
+Supramolecule #3: T4 Bacteriophage Clamp Loader (gp44 + gp62)
+Supramolecule #4: T4 Bacteriophage Clamp Loader subunit A (gp62)
+Supramolecule #5: T4 Bacteriophage Clamp Loader subunits B,C,D,E(gp44)
+Supramolecule #6: primed DNA duplex
+Macromolecule #1: primer DNA
+Macromolecule #2: template DNA
+Macromolecule #3: Sliding clamp
+Macromolecule #4: Sliding-clamp-loader large subunit
+Macromolecule #5: Sliding-clamp-loader small subunit
+Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-...
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
---|---|
Output model | PDB-8unf: |