+Open data
-Basic information
Entry | Database: PDB / ID: 8efy | ||||||
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Title | Structure of double homo-hexameric AAA+ ATPase RuvB motors | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Holliday Junction / AAA+ ATPase / RuvB / Homo-hexamer / DNA recombination | ||||||
Function / homology | Function and homology information Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA helicase / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | ||||||
Authors | Shen, Z.F. / Rish, A.D. / Fu, T.M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of double homo-hexameric AAA+ ATPase RuvB motor binding with DNA substrate Authors: Rish, A.D. / Shen, Z.F. / Fu, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8efy.cif.gz | 753 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8efy.ent.gz | 623.6 KB | Display | PDB format |
PDBx/mmJSON format | 8efy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/8efy ftp://data.pdbj.org/pub/pdb/validation_reports/ef/8efy | HTTPS FTP |
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-Related structure data
Related structure data | 28107MC 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 , 1 types, 12 molecules ABCDEFIJKLMN
#1: Protein | Mass: 36024.688 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: ruvB, TTHA0406 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SL87, DNA helicase |
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-DNA chain , 2 types, 4 molecules GOHP
#2: DNA chain | Mass: 15146.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria) #3: DNA chain | Mass: 15691.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB8 (bacteria) |
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-Non-polymers , 3 types, 20 molecules
#4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-AGS / |
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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 |
-Sample preparation
Component | Name: Double homo-hexameric AAA+ ATPase RuvB motors / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 326270 / Symmetry type: POINT | ||||||||||||||||||||||||
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