- EMDB-8728: CryoEM Structure of the Zinc Transporter YiiP from helical crystals -
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Basic information
Entry
Database: EMDB / ID: EMD-8728
Title
CryoEM Structure of the Zinc Transporter YiiP from helical crystals
Map data
primary map
Sample
Complex: YiiP dimer in an inward-facing conformation
Protein or peptide: Cadmium and zinc efflux pump FieF
Ligand: ZINC ION
Keywords
zinc antiporter / membrane protein / cation diffusion facilitator / metal transport / helical crystals / Structural Genomics / PSI-Biology / Transcontinental EM Initiative for Membrane Protein Structure / TEMIMPS
Function / homology
Function and homology information
zinc efflux active transmembrane transporter activity / cadmium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / intracellular zinc ion homeostasis / metal ion binding / plasma membrane Similarity search - Function
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
U54 GM94598
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM095747
United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Structural basis for the alternating access mechanism of the cation diffusion facilitator YiiP. Authors: Maria Luisa Lopez-Redondo / Nicolas Coudray / Zhening Zhang / John Alexopoulos / David L Stokes / Abstract: YiiP is a dimeric antiporter from the cation diffusion facilitator family that uses the proton motive force to transport Zn across bacterial membranes. Previous work defined the atomic structure of ...YiiP is a dimeric antiporter from the cation diffusion facilitator family that uses the proton motive force to transport Zn across bacterial membranes. Previous work defined the atomic structure of an outward-facing conformation, the location of several Zn binding sites, and hydrophobic residues that appear to control access to the transport sites from the cytoplasm. A low-resolution cryo-EM structure revealed changes within the membrane domain that were associated with the alternating access mechanism for transport. In the current work, the resolution of this cryo-EM structure has been extended to 4.1 Å. Comparison with the X-ray structure defines the differences between inward-facing and outward-facing conformations at an atomic level. These differences include rocking and twisting of a four-helix bundle that harbors the Zn transport site and controls its accessibility within each monomer. As previously noted, membrane domains are closely associated in the dimeric structure from cryo-EM but dramatically splayed apart in the X-ray structure. Cysteine crosslinking was used to constrain these membrane domains and to show that this large-scale splaying was not necessary for transport activity. Furthermore, dimer stability was not compromised by mutagenesis of elements in the cytoplasmic domain, suggesting that the extensive interface between membrane domains is a strong determinant of dimerization. As with other secondary transporters, this interface could provide a stable scaffold for movements of the four-helix bundle that confers alternating access of these ions to opposite sides of the membrane.
History
Deposition
May 10, 2017
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Header (metadata) release
Jul 26, 2017
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Map release
Mar 14, 2018
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Update
Mar 13, 2024
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Current status
Mar 13, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Applied symmetry - Helical parameters - Δz: 28.2 Å Applied symmetry - Helical parameters - Δ&Phi: -17.0 ° Applied symmetry - Helical parameters - Axial symmetry: D5 (2x5 fold dihedral) Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) Details: Reconstruction was achieved using the IHRSR method implemented in RELION 2.0. Number images used: 72333
Segment selection
Number selected: 141904 Software:
Name
details
SPARX/EMAN2 (ver. EMAN2.1)
sxhelixboxer.py
RELION (ver. 2.0)
2D Classissification
Details: 2293 filaments selected with SPARX/EMAN2, then windowed into 141,904 segments (450x450 pixel overlapping segments)
Startup model
Type of model: OTHER Details: A map was obtained previously with images acquired on a JEOL2100 microscope. This map was used as a startup model (That map was obtained as follow: we started with a noisy cylinder. Then, a ...Details: A map was obtained previously with images acquired on a JEOL2100 microscope. This map was used as a startup model (That map was obtained as follow: we started with a noisy cylinder. Then, a first reconstruction was obtained with Helicon (from SPARX) and refined with Frealix).
Final angle assignment
Type: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
chain_id: B, residue_range: 7-288, source_name: PDB, initial_model_type: experimental model
Details
The residues were manually adjusted in COOT relying on the large side-chain residues, and the whole system was further optimized using the real_space_refine algorithm in Phenix to ensure proper fit. The conformation was subjected to 13 rounds of COOT/Phenix refinements.
Refinement
Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model
PDB-5vrf: CryoEM Structure of the Zinc Transporter YiiP from helical crystals
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