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- EMDB-9316: Dihedral oligomeric complex of GyrA N-terminal fragment with DNA,... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9316 | ||||||||||||||||||
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Title | Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetry | ||||||||||||||||||
![]() | Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetry | ||||||||||||||||||
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![]() | topoisomerase / oligomeric complex / DNA complex / gyrase / T-segment / ISOMERASE-DNA complex | ||||||||||||||||||
Function / homology | ![]() DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.35 Å | ||||||||||||||||||
![]() | Soczek KM / Grant T | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 42.4 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n1pMC ![]() 9317C ![]() 9318C ![]() 6n1qC ![]() 6n1rC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of DNA Gyrase A subunit with DNA in C2 symmetry
Entire | Name: Complex of DNA Gyrase A subunit with DNA in C2 symmetry |
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Components |
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-Supramolecule #1: Complex of DNA Gyrase A subunit with DNA in C2 symmetry
Supramolecule | Name: Complex of DNA Gyrase A subunit with DNA in C2 symmetry type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 490 KDa |
-Supramolecule #2: DNA Gyrase A
Supramolecule | Name: DNA Gyrase A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Cloning vector pBR322 (others) |
-Macromolecule #1: DNA gyrase subunit A
Macromolecule | Name: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ec: 5.99.1.3 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 57.977578 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHSSG VDLGTENLYF QSIAMQDKNL VNVNLTKEMK ASFIDYAMSV IVARALPDVR DGLKPVHRRI LYGMNELGVT PDKPHKKSA RITGDVMGKY HPHGDSSIYE AMVRMAQWWS YRYMLVDGHG NFGSMDGDSA AAQRYTEARM SKIALEMLRD I NKNTVDFV ...String: MHHHHHHSSG VDLGTENLYF QSIAMQDKNL VNVNLTKEMK ASFIDYAMSV IVARALPDVR DGLKPVHRRI LYGMNELGVT PDKPHKKSA RITGDVMGKY HPHGDSSIYE AMVRMAQWWS YRYMLVDGHG NFGSMDGDSA AAQRYTEARM SKIALEMLRD I NKNTVDFV DNYDANEREP LVLPARFPNL LVNGATGIAV GMATNIPPHN LGETIDAVKL VMDNPEVTTK DLMEVLPGPD FP TGALVMG KSGIHKAYET GKGSIVLRSR TEIETTKTGR ERIVVTEFPY MVNKTKVHEH IVRLVQEKRI EGITAVRDES NRE GVRFVI EVKRDASANV ILNNLFKMTQ MQTNFGFNML AIQNGIPKIL SLRQILDAYI EHQKEVVVRR TRFDKEKAEA RAHI LEGLL IALDHIDEVI RIIRASETDA EAQAELMSKF KLSERQSQAI LDMRLRRLTG LERDKIQSEY DDLLALIADL ADILA KPER VSQIIKDELD EVKRKFSDKR RTELMVG UniProtKB: DNA gyrase subunit A |
-Macromolecule #2: DNA (44-MER)
Macromolecule | Name: DNA (44-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Cloning vector pBR322 (others) |
Molecular weight | Theoretical: 13.641771 KDa |
Sequence | String: (DG)(DA)(DG)(DA)(DA)(DG)(DA)(DA)(DT)(DC) (DA)(DT)(DA)(DA)(DT)(DG)(DG)(DG)(DG)(DA) (DA)(DG)(DG)(DC)(DC)(DA)(DT)(DC)(DC) (DA)(DG)(DC)(DC)(DT)(DC)(DG)(DC)(DG)(DT) (DC) (DG)(DC)(DG)(DA) |
-Macromolecule #3: DNA (44-MER)
Macromolecule | Name: DNA (44-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Cloning vector pBR322 (others) |
Molecular weight | Theoretical: 13.4586 KDa |
Sequence | String: (DT)(DC)(DG)(DC)(DG)(DA)(DC)(DG)(DC)(DG) (DA)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DT)(DG) (DG)(DC)(DC)(DT)(DT)(DC)(DC)(DC)(DC) (DA)(DT)(DT)(DA)(DT)(DG)(DA)(DT)(DT)(DC) (DT) (DT)(DC)(DT)(DC) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL 3200FS |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Number real images: 718 / Average exposure time: 12.0 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 40323 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 2-486 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient |
Output model | ![]() PDB-6n1p: |