Inward-Facing Conformation of the Zinc Transporter YiiP revealed by Cryo-electron Microscopy
ELECTRON MICROSCOPY
Sample
YiiP from Shewanella oneidensis in DOPG lipids
Specimen Preparation
Sample Aggregation State
2D ARRAY
Vitrification Instrument
GATAN CRYOPLUNGE 3
Cryogen Name
ETHANE
Sample Vitrification Details
Blot for 2-5 seconds before plunging into liquid ethane (Gatan cryoplunger)
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
Reported Resolution (Å)
13
Resolution Method
Other Details
CRYSTAL CELL PARAMETERS WERE A=57.5, B=34.0, C=100.0, ALPHA=90, BETA=90, GAMMA=85.3.
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
D3
Axial Rise
17.1
Angular Rotation
56.4
Map-Model Fitting and Refinement
Id
1 (3H90)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
METHOD--MDFF DETAILS--An initial homology model of YiiP from S. oneidensis was
built with MODELLER 9v7 using the X-ray crystal structure of YiiP from ...
METHOD--MDFF DETAILS--An initial homology model of YiiP from S. oneidensis was
built with MODELLER 9v7 using the X-ray crystal structure of YiiP from E. coli
(PDB entry 3H90) as a template. This model included 9 residues at the
N-terminus and 4 residues at the C-terminus that were not present in the X-ray
structure. Initial configurations were obtained by manually placing the
symmetry axis of the homology model onto the symmetry axis of the electron
density map and aligning the protein C-terminal domains to the corresponding
densities. In the first step of the MDFF fitting, harmonic potentials were
applied to (a) the four-helix bundle formed by helices M1, M2, M4, and M5
(residues 12-32, 42-65, 119-142, and 147-165, respectively), (b) the M3 and M6
helices at the dimeric interface (residues 78-108 and 179-211, respectively),
and (c) the C-terminal intracellular domain (residues 212-297).
