3J1Z

Inward-Facing Conformation of the Zinc Transporter YiiP revealed by Cryo-electron Microscopy

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H90

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).

Data Acquisition
Detector Type	GENERIC FILM
Electron Dose (electrons/Å**2)	10

Imaging Experiment	1
Date of Experiment	2009-02-10
Temperature (Kelvin)	100
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	1600
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.1
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	50000
Calibrated Magnification	51190
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
RECONSTRUCTION	EMIP
RECONSTRUCTION	SPARX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Corrected throughout the reconstruction cycle

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.