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- PDB-5n9y: The full-length structure of ZntB -

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Basic information

Entry
Database: PDB / ID: 5n9y
TitleThe full-length structure of ZntB
ComponentsZinc transport protein ZntBZinc transporter protein
KeywordsMEMBRANE PROTEIN / ZntB / zinc transport / CorA
Function / homology
Function and homology information


zinc efflux transmembrane transporter activity / zinc ion import across plasma membrane / solute:proton symporter activity / zinc ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / zinc ion transmembrane transport / magnesium ion transmembrane transporter activity / cobalt ion binding / plasma membrane => GO:0005886 / magnesium ion binding
Similarity search - Function
Zinc transport protein ZntB / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Zinc transport protein ZntB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsCornelius, G. / Stetsenko, A. / Scheres, S.H.W. / Slotboom, D.J. / Guskov, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWO723.014.002 Netherlands
CitationJournal: Nat Commun / Year: 2017
Title: The structural basis of proton driven zinc transport by ZntB.
Authors: Cornelius Gati / Artem Stetsenko / Dirk J Slotboom / Sjors H W Scheres / Albert Guskov /
Abstract: Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc ...Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc concentration have evolved. In Enterobacteriaceae, several membrane transporters are involved in zinc homeostasis and linked to virulence. ZntB has been proposed to play a role in the export of zinc, but the transport mechanism of ZntB is poorly understood and based only on experimental characterization of its distant homologue CorA magnesium channel. Here, we report the cryo-electron microscopy structure of full-length ZntB from Escherichia coli together with the results of isothermal titration calorimetry, and radio-ligand uptake and fluorescent transport assays on ZntB reconstituted into liposomes. Our results show that ZntB mediates Zn uptake, stimulated by a pH gradient across the membrane, using a transport mechanism that does not resemble the one proposed for homologous CorA channels.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: Zinc transport protein ZntB
B: Zinc transport protein ZntB
C: Zinc transport protein ZntB
D: Zinc transport protein ZntB
E: Zinc transport protein ZntB


Theoretical massNumber of molelcules
Total (without water)183,2605
Polymers183,2605
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22460 Å2
ΔGint-113 kcal/mol
Surface area72250 Å2
MethodPISA

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Components

#1: Protein
Zinc transport protein ZntB / Zinc transporter protein


Mass: 36652.082 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: zntB, ydaN, b1342, JW1336 / Production host: Escherichia coli (E. coli) / References: UniProt: P64423

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentameric zntb transporter / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333490 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00813085
ELECTRON MICROSCOPYf_angle_d1.27217760
ELECTRON MICROSCOPYf_dihedral_angle_d10.7197860
ELECTRON MICROSCOPYf_chiral_restr0.0682005
ELECTRON MICROSCOPYf_plane_restr0.0092315

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