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- EMDB-9318: Tetrahedral oligomeric complex of GyrA N-terminal fragment, solve... -

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Basic information

Entry
Database: EMDB / ID: EMD-9318
TitleTetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetry
Map dataTetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetry
Sample
  • Complex: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, solved by cryoEM in T symmetry
    • Protein or peptide: DNA gyrase subunit A
Keywordstopoisomerase / oligomeric complex / gyrase / ISOMERASE
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
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesStreptococcus pneumoniae G54 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSoczek KM / Grant T
Funding support United States, United Kingdom, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM051350 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118108 United States
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Cancer Research UKFC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
CitationJournal: 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
DepositionNov 10, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseDec 5, 2018-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0374
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0374
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n1r
  • Surface level: 0.0374
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9318.png

Downloads & links

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Map

FileDownload / File: emd_9318.map.gz / Format: CCP4 / Size: 78.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 274 pix.
= 284.96 Å		1.04 Å/pix.
x 274 pix.
= 284.96 Å		1.04 Å/pix.
x 274 pix.
= 284.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0374 / Movie #1: 0.0374
Minimum - Maximum-0.084237345 - 0.16272984
Average (Standard dev.)0.0010195948 (±0.009135741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions274274274
Spacing274274274
CellA=B=C: 284.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z274274274
origin x/y/z0.0000.0000.000
length x/y/z284.960284.960284.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS274274274
D min/max/mean-0.0840.1630.001

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Supplemental data

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Sample components

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Entire : Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, ...

EntireName: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, solved by cryoEM in T symmetry
Components
  • Complex: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, solved by cryoEM in T symmetry
    • Protein or peptide: DNA gyrase subunit A

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Supramolecule #1: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, ...

SupramoleculeName: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, solved by cryoEM in T symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae G54 (bacteria)
Molecular weightTheoretical: 695 KDa

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Macromolecule #1: DNA gyrase subunit A

MacromoleculeName: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: ec: 5.99.1.3
Source (natural)Organism: Streptococcus pneumoniae G54 (bacteria)
Molecular weightTheoretical: 57.977578 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
55.0 mMpotassium chlorideKCl
10.0 mMstrontium chlorideSrCl2
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K / Max: 100.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm 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: 4265 / Average exposure time: 14.0 sec. / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 46430 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1205406
Startup modelType of model: OTHER / Details: common line method
Final reconstructionNumber classes used: 61 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 673694
Initial angle assignmentType: COMMON LINE / Software - Name: IMAGIC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 96 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4z2c


Chain - Chain ID: A / Chain - Residue range: 2-486 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient
Output model

PDB-6n1r:
Tetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetry

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