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- PDB-3j1z: Inward-Facing Conformation of the Zinc Transporter YiiP revealed ... -

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Entry
Database: PDB / ID: 3j1z
TitleInward-Facing Conformation of the Zinc Transporter YiiP revealed by Cryo-electron Microscopy
ComponentsCation efflux family protein
KeywordsMETAL TRANSPORT / zinc transporter / secondary transporter / alternating access mechanism / 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
Cation efflux protein, cytoplasmic domain / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
Cation-efflux pump FieF
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 13 Å
AuthorsCoudray, N. / Valvo, S. / Hu, M. / Lasala, R. / Kim, C. / Vink, M. / Zhou, M. / Provasi, D. / Filizola, M. / Tao, J. ...Coudray, N. / Valvo, S. / Hu, M. / Lasala, R. / Kim, C. / Vink, M. / Zhou, M. / Provasi, D. / Filizola, M. / Tao, J. / Fang, J. / Penczek, P.A. / Ubarretxena-Belandia, I. / Stokes, D.L. / Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS)
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.
Authors: Nicolas Coudray / Salvatore Valvo / Minghui Hu / Ralph Lasala / Changki Kim / Martin Vink / Ming Zhou / Davide Provasi / Marta Filizola / Juoehi Tao / Jia Fang / Pawel A Penczek / Iban ...Authors: Nicolas Coudray / Salvatore Valvo / Minghui Hu / Ralph Lasala / Changki Kim / Martin Vink / Ming Zhou / Davide Provasi / Marta Filizola / Juoehi Tao / Jia Fang / Pawel A Penczek / Iban Ubarretxena-Belandia / David L Stokes /
Abstract: YiiP is a dimeric Zn(2+)/H(+) antiporter from Escherichia coli belonging to the cation diffusion facilitator family. We used cryoelectron microscopy to determine a 13-Å resolution structure of a ...YiiP is a dimeric Zn(2+)/H(+) antiporter from Escherichia coli belonging to the cation diffusion facilitator family. We used cryoelectron microscopy to determine a 13-Å resolution structure of a YiiP homolog from Shewanella oneidensis within a lipid bilayer in the absence of Zn(2+). Starting from the X-ray structure in the presence of Zn(2+), we used molecular dynamics flexible fitting to build a model consistent with our map. Comparison of the structures suggests a conformational change that involves pivoting of a transmembrane, four-helix bundle (M1, M2, M4, and M5) relative to the M3-M6 helix pair. Although accessibility of transport sites in the X-ray model indicates that it represents an outward-facing state, our model is consistent with an inward-facing state, suggesting that the conformational change is relevant to the alternating access mechanism for transport. Molecular dynamics simulation of YiiP in a lipid environment was used to address the feasibility of this conformational change. Association of the C-terminal domains is the same in both states, and we speculate that this association is responsible for stabilizing the dimer that, in turn, may coordinate the rearrangement of the transmembrane helices.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Structure summary
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Feb 13, 2013Group: Database references
Revision 1.4Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
P: Cation efflux family protein
Q: Cation efflux family protein


Theoretical massNumber of molelcules
Total (without water)67,7332
Polymers67,7332
Non-polymers00
Water00
1
P: Cation efflux family protein
Q: Cation efflux family protein
x 18


Theoretical massNumber of molelcules
Total (without water)1,219,20036
Polymers1,219,20036
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation17
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
SymmetryHelical symmetry: (Circular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 18 / Rise per n subunits: 17.1 Å / Rotation per n subunits: 56.4 °)
DetailsTHE SYMMETRY OF THE HELIX IS D3.

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Components

#1: Protein Cation efflux family protein / YiiP / Ferrous-iron efflux pump (Fief)


Mass: 33866.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_4475 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8E919

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: YiiP from Shewanella oneidensis in DOPG lipids / Type: COMPLEX
Buffer solutionName: 20mM TES, 5mM MgCl2, 100mM NaCl, 5mM NaN3 / pH: 7 / Details: 20mM TES, 5mM MgCl2, 100mM NaCl, 5mM NaN3
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon grid
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 100 K
Details: Blot for 2-5 seconds before plunging into liquid ethane (Gatan cryoplunger)
Method: Blot for 2-5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 10, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51190 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 nm / Cs: 2.1 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GENERIC FILM / Details: Kodak SO163 film
Image scansNum. digital images: 19
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMIP3D reconstruction
2SPARX3D reconstruction
CTF correctionDetails: Corrected throughout the reconstruction cycle
Helical symmertyAngular rotation/subunit: 56.4 ° / Axial rise/subunit: 17.1 Å / Axial symmetry: D3
3D reconstructionMethod: IHRSR / Resolution: 13 Å / Actual pixel size: 2.735 Å
Details: CRYSTAL CELL PARAMETERS WERE A=57.5, B=34.0, C=100.0, ALPHA=90, BETA=90, GAMMA=85.3.
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
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 E. coli (PDB entry 3H90) as a template. ...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 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).
Atomic model buildingPDB-ID: 3H90

3h90


Accession code: 3H90 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 0 0 4586

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