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- PDB-9go3: Sub-open structure of the mechanosensitive channel YbiO -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9go3
TitleSub-open structure of the mechanosensitive channel YbiO
ComponentsMechanosensitive channel protein
KeywordsMEMBRANE PROTEIN / Mechanosensitive / MscS-like / YbiO
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / plasma membrane
Similarity search - Function
Mechanosensitive ion channel YbiO / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily
Similarity search - Domain/homology
Mechanosensitive channel protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLane, B.J. / Pliotas, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S018069/1 United Kingdom
Wellcome Trust219999/Z/19/Z United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Sub-open structure of the mechanosensitive channel YbiO
Authors: Lane, B.J. / Pliotas, C.
History
DepositionSep 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mechanosensitive channel protein
B: Mechanosensitive channel protein
C: Mechanosensitive channel protein
D: Mechanosensitive channel protein
E: Mechanosensitive channel protein
F: Mechanosensitive channel protein
G: Mechanosensitive channel protein


Theoretical massNumber of molelcules
Total (without water)581,3337
Polymers581,3337
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Mechanosensitive channel protein / Membrane protein YbiO / Moderate conductance mechanosensitive channel YbiO


Mass: 83047.555 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ybiO, ACU57_05830, BANRA_04892, BCB93_001408, BGM66_000969, BvCmsKKP061_03136, CIG67_24150, CTR35_001344, DS732_09015, E4K51_02825, EIZ93_04895, F9461_01290, FGAF848_14890, FWK02_02255, G3V95_ ...Gene: ybiO, ACU57_05830, BANRA_04892, BCB93_001408, BGM66_000969, BvCmsKKP061_03136, CIG67_24150, CTR35_001344, DS732_09015, E4K51_02825, EIZ93_04895, F9461_01290, FGAF848_14890, FWK02_02255, G3V95_03395, G4A38_09710, G4A47_02540, GNW61_02400, GOP25_10155, GQM21_08905, GRW05_01565, HMV95_02535, HVY77_17790, J0541_000991, JNP96_08445, NCTC8500_03704, NCTC9045_03925, NCTC9706_00705, P6223_001677, QDW62_18320, RZR61_20830, SAMEA3752557_02230, WR15_25365
Production host: Escherichia coli (E. coli) / Strain (production host): MJF612 / References: UniProt: W8SQ51
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MscS-like core of YbiO in GDN/CHS detergent / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: MJF612
Buffer solutionpH: 7.4
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 66.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
4RELION3.1CTF correction
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
12cryoSPARC3.3.1classification
13cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147935 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212362
ELECTRON MICROSCOPYf_angle_d0.45916891
ELECTRON MICROSCOPYf_dihedral_angle_d3.8781841
ELECTRON MICROSCOPYf_chiral_restr0.0422079
ELECTRON MICROSCOPYf_plane_restr0.0032226

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