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- PDB-7raz: Small conductance mechanosensitive channel MscS -

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Basic information

Entry
Database: PDB / ID: 7raz
TitleSmall conductance mechanosensitive channel MscS
ComponentsSmall-conductance mechanosensitive channel
KeywordsTRANSPORT PROTEIN / small conductance mechanosensitive channel MscS / NCMN / ion channel / membrane protein
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / protein homooligomerization / monoatomic ion transmembrane transport / identical protein binding / membrane / plasma membrane
Similarity search - Function
Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal ...Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / Mechanosensitive ion channel MscS, archaea/bacteria type / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / 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 / Alpha-Beta Plaits - #100 / LSM domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.4 Å
AuthorsCatalano, C. / Ben-Hail, D. / Qiu, W. / des Georges, A. / Guo, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM133598 United States
CitationJournal: To Be Published
Title: Small conductance mechanosensitive channel MscS
Authors: Catalano, C. / Ben-Hail, D. / Qiu, W. / des Georges, A. / Guo, Y.
History
DepositionJul 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small-conductance mechanosensitive channel
B: Small-conductance mechanosensitive channel
C: Small-conductance mechanosensitive channel
D: Small-conductance mechanosensitive channel
E: Small-conductance mechanosensitive channel
F: Small-conductance mechanosensitive channel
G: Small-conductance mechanosensitive channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,59914
Polymers216,4607
Non-polymers5,1387
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Small-conductance mechanosensitive channel / MscS


Mass: 30922.898 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21-Gold(DE3)pLysS AG / Gene: mscS, yggB, b2924, JW2891
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P0C0S1
#2: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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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: Small conductance mechanosensitive channel MscS / Type: CELL / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: 2% uranyl acetate
Specimen supportGrid type: UltrAuFoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 10 sec. / Electron dose: 61.05 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1352
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2Leginonimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 500000
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275000 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 2OAU

2oau


Accession code: 2OAU / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410612
ELECTRON MICROSCOPYf_angle_d0.58114322
ELECTRON MICROSCOPYf_dihedral_angle_d5.4971596
ELECTRON MICROSCOPYf_chiral_restr0.0431666
ELECTRON MICROSCOPYf_plane_restr0.0031827

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