[English] 日本語
Yorodumi
- PDB-6n1r: Tetrahedral oligomeric complex of GyrA N-terminal fragment, solve... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6n1r
TitleTetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetry
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / topoisomerase / oligomeric complex / gyrase
Function / homologyDNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase/topoisomerase IV, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / DNA topoisomerase, type IIA, subunit A/ C-terminal, alpha-beta / DNA topoisomerase, type IIA, subunit A/C-terminal / Type IIA DNA topoisomerase subunit A, alpha-helical domain superfamily / DNA topoisomerase type II (ATP-hydrolyzing) activity ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase/topoisomerase IV, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / DNA topoisomerase, type IIA, subunit A/ C-terminal, alpha-beta / DNA topoisomerase, type IIA, subunit A/C-terminal / Type IIA DNA topoisomerase subunit A, alpha-helical domain superfamily / DNA topoisomerase type II (ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-dependent DNA replication / chromosome / DNA binding / ATP binding / cytoplasm / DNA gyrase subunit A
Function and homology information
Specimen sourceStreptococcus pneumoniae G54 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsSoczek, K.M. / Grant, T. / Rosenthal, P.B. / Mondragon, A.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2018 / Release: Dec 5, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9318
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit A
C: DNA gyrase subunit A
D: DNA gyrase subunit A
E: DNA gyrase subunit A
F: DNA gyrase subunit A
G: DNA gyrase subunit A
H: DNA gyrase subunit A
I: DNA gyrase subunit A
J: DNA gyrase subunit A
K: DNA gyrase subunit A
L: DNA gyrase subunit A


Theoretical massNumber of molelcules
Total (without water)695,73112
Polyers695,73112
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)37980
ΔGint (kcal/M)-223
Surface area (Å2)268910

-
Components

#1: Protein/peptide
DNA gyrase subunit A /


Mass: 57977.578 Da / Num. of mol.: 12 / Fragment: UNP residues 20-506
Source: (gene. exp.) Streptococcus pneumoniae G54 (bacteria)
Gene: gyrA_1, gyrA, ERS409327_01712 / Plasmid name: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0Y2BJX7, DNA topoisomerase (ATP-hydrolysing)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Tetrahedral complex of DNA Gyrase A subunit N-terminal fragment, solved by cryoEM in T symmetry
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.695 MDa / Experimental value: NO
Source (natural)Organism: Streptococcus pneumoniae G54 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pMCSG7
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
150 mMTris1
255 mMpotassium chlorideKCl1
310 mMstrontium chlorideSrCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 / Calibrated magnification: 46430 / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 kelvins / Temperature (min): 100 kelvins
Image recordingAverage exposure time: 14 sec. / Electron dose: 74 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 4265
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansSampling size: 5 microns / Width: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 1-40

-
Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7MDFF0.4model fitting
9IMAGICinitial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13REFMAC5model refinement
14PHENIX1.12-2829model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1205406
SymmetryPoint symmetry: T
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 673694 / Algorithm: FOURIER SPACE / Number of class averages: 61 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 4Z2C
Pdb chain ID: A / Pdb chain residue range: 2-486

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more