+Open data
-Basic information
Entry | Database: PDB / ID: 6pwn | ||||||
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Title | MscS Nanodisc with N-terminal His-Tag | ||||||
Components | Small-conductance mechanosensitive channel | ||||||
Keywords | MEMBRANE PROTEIN / MscS / Nanodisc / Mechanosensitive Channel of Small Conductance / Mechanosensitive / Channel | ||||||
Function / homology | Function and homology information intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Reddy, B.G. / Perozo, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2019 Title: Molecular basis of force-from-lipids gating in the mechanosensitive channel MscS. Authors: Bharat Reddy / Navid Bavi / Allen Lu / Yeonwoo Park / Eduardo Perozo / Abstract: Prokaryotic mechanosensitive (MS) channels open by sensing the physical state of the membrane. As such, lipid-protein interactions represent the defining molecular process underlying ...Prokaryotic mechanosensitive (MS) channels open by sensing the physical state of the membrane. As such, lipid-protein interactions represent the defining molecular process underlying mechanotransduction. Here, we describe cryo-electron microscopy (cryo-EM) structures of the small-conductance mechanosensitive channel (MscS) in nanodiscs (ND). They reveal a novel membrane-anchoring fold that plays a significant role in channel activation and establish a new location for the lipid bilayer, shifted ~14 Å from previous consensus placements. Two types of lipid densities are explicitly observed. A phospholipid that 'hooks' the top of each TM2-TM3 hairpin and likely plays a role in force sensing, and a bundle of acyl chains occluding the permeation path above the L105 cuff. These observations reshape our understanding of force-from-lipids gating in MscS and highlight the key role of allosteric interactions between TM segments and phospholipids bound to key dynamic components of the channel. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pwn.cif.gz | 337.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pwn.ent.gz | 279.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pwn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6pwn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6pwn_validation.xml.gz | 70.2 KB | Display | |
Data in CIF | 6pwn_validation.cif.gz | 90.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/6pwn ftp://data.pdbj.org/pub/pdb/validation_reports/pw/6pwn | HTTPS FTP |
-Related structure data
Related structure data | 20508MC 6pwoC 6pwpC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10496 (Title: MscS Nanodisc with N-terminal His-Tag / Data size: 762.3 Data #1: MscS Nanodisc with N-terminal His-Tag [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 33094.258 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: mscS, yggB, b2924, JW2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S1 #2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-R16 / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mechanosensitive Channel of Small Conductance / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: 22C. Blot Force 3 for 3 seconds. Double application with a blotting between applications. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 50 |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 3.0.6 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372870 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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