5AJI | pdb_00005aji

MscS D67R1 high resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 
    0.263 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5AJI

This is version 1.3 of the entry. See complete history

Literature

The Role of Lipids in Mechanosensation.

Pliotas, C.Dahl, A.C.E.Rasmussen, T.Mahendran, K.R.Smith, T.K.Marius, P.Gault, J.Banda, T.Rasmussen, A.Miller, S.Robinson, C.V.Bayley, H.Sansom, M.S.P.Booth, I.R.Naismith, J.H.

(2015) Nat Struct Mol Biol 22: 991

  • DOI: https://doi.org/10.1038/nsmb.3120
  • Primary Citation Related Structures: 
    5AJI

  • PubMed Abstract: 

    The ability of proteins to sense membrane tension is pervasive in biology. A higher-resolution structure of the Escherichia coli small-conductance mechanosensitive channel MscS identifies alkyl chains inside pockets formed by the transmembrane helices (TMs). Purified MscS contains E. coli lipids, and fluorescence quenching demonstrates that phospholipid acyl chains exchange between bilayer and TM pockets. Molecular dynamics and biophysical analyses show that the volume of the pockets and thus the number of lipid acyl chains within them decreases upon channel opening. Phospholipids with one acyl chain per head group (lysolipids) displace normal phospholipids (with two acyl chains) from MscS pockets and trigger channel opening. We propose that the extent of acyl-chain interdigitation in these pockets determines the conformation of MscS. When interdigitation is perturbed by increased membrane tension or by lysolipids, the closed state becomes unstable, and the channel gates.


  • Organizational Affiliation
    • Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK.

Macromolecule Content 

  • Total Structure Weight: 219.18 kDa 
  • Atom Count: 13,963 
  • Modeled Residue Count: 1,809 
  • Deposited Residue Count: 2,002 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
A, B, C, D, E
A, B, C, D, E, F, G
286Escherichia coliMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0S1 (Escherichia coli (strain K12))
Explore P0C0S1 
Go to UniProtKB:  P0C0S1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0S1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D10

Query on D10



Download:Ideal Coordinates CCD File
L [auth C],
O [auth D],
V [auth G]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
H [auth A],
Q [auth E]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX

Query on HEX



Download:Ideal Coordinates CCD File
I [auth A]
J [auth B]
K [auth B]
M [auth C]
N [auth C]
I [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
R [auth E],
S [auth E],
T [auth F],
U [auth F]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
R1A
Query on R1A
A, B, C, D, E
A, B, C, D, E, F, G
L-PEPTIDE LINKINGC12 H21 N2 O3 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free:  0.263 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.33α = 90
b = 149.09β = 90
c = 173.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-12-23
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description