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Yorodumi- PDB-6n1r: Tetrahedral oligomeric complex of GyrA N-terminal fragment, solve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n1r | ||||||||||||||||||
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Title | Tetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetry | ||||||||||||||||||
Components | DNA gyrase subunit A | ||||||||||||||||||
Keywords | ISOMERASE / topoisomerase / oligomeric complex / gyrase | ||||||||||||||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Streptococcus pneumoniae G54 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||||||||||||||
Authors | Soczek, K.M. / Grant, T. / Rosenthal, P.B. / Mondragon, A. | ||||||||||||||||||
Funding support | United States, United Kingdom, 5items
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Citation | Journal: Elife / Year: 2018 Title: CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage. Authors: Katarzyna M Soczek / Tim Grant / Peter B Rosenthal / Alfonso Mondragón / Abstract: Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of ...Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6n1r.cif.gz | 959.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n1r.ent.gz | 777.1 KB | Display | PDB format |
PDBx/mmJSON format | 6n1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n1r_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6n1r_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6n1r_validation.xml.gz | 166.3 KB | Display | |
Data in CIF | 6n1r_validation.cif.gz | 240.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/6n1r ftp://data.pdbj.org/pub/pdb/validation_reports/n1/6n1r | HTTPS FTP |
-Related structure data
Related structure data | 9318MC 9316C 9317C 6n1pC 6n1qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 57977.578 Da / Num. of mol.: 12 / Fragment: UNP residues 20-506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae G54 (bacteria) Gene: gyrA_1, gyrA, ERS409327_01712 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0Y2BJX7, UniProt: Q8DPM2*PLUS, EC: 5.99.1.3 |
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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: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, solved by cryoEM in T symmetry Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.695 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Streptococcus pneumoniae G54 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pMCSG7 | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 46430 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K |
Image recording | Average exposure time: 14 sec. / Electron dose: 74 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4265 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1205406 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: T (tetrahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 673694 / Algorithm: FOURIER SPACE / Num. of class averages: 61 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4Z2C Pdb chain-ID: A / Accession code: 4Z2C / Pdb chain residue range: 2-486 / Source name: PDB / Type: experimental model |