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- EMDB-3605: The full-length structure of ZntB -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-3605
TitleThe full-length structure of ZntB
Map data
Sample
  • Complex: Pentameric zntb transporter
    • Protein or peptide: Zinc transport protein ZntB
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 / magnesium ion binding / plasma membrane
Similarity search - Function
Zinc transport protein ZntB / Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Zinc transport protein ZntB
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsCornelius G / Stetsenko A / Scheres SHW / Slotboom DJ / Guskov A
Funding support Netherlands, 1 items
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, 2017-
Header (metadata) releaseMar 22, 2017-
Map releaseNov 15, 2017-
UpdateOct 23, 2019-
Current statusOct 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0269
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0269
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5n9y
  • Surface level: 0.0269
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3605.png

Downloads & links

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Map

FileDownload / File: emd_3605.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 180 pix.
= 257.4 Å		1.43 Å/pix.
x 180 pix.
= 257.4 Å		1.43 Å/pix.
x 180 pix.
= 257.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0269 / Movie #1: 0.0269
Minimum - Maximum-0.08467929 - 0.17267512
Average (Standard dev.)0.00078010594 (±0.006432195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 257.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z257.400257.400257.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0850.1730.001

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Supplemental data

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Sample components

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Entire : Pentameric zntb transporter

EntireName: Pentameric zntb transporter
Components
  • Complex: Pentameric zntb transporter
    • Protein or peptide: Zinc transport protein ZntB

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Supramolecule #1: Pentameric zntb transporter

SupramoleculeName: Pentameric zntb transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Zinc transport protein ZntB

MacromoleculeName: Zinc transport protein ZntB / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 36.652082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEAIKGSDVN VPDAVFAWML DGRGGVKPLE NTDVIDEAHP CWLHLNYVHH DSAQWLATTP LLPNNVRDAL AGESTRPRVS RLGEGTLIT LRCINGSTDE RPDQLVAMRV YMDGRLIVST RQRKVLALDD VVSDLEEGTG PTDCGGWLVD VCDALTDHSS E FIEQLHDK ...String:
MEAIKGSDVN VPDAVFAWML DGRGGVKPLE NTDVIDEAHP CWLHLNYVHH DSAQWLATTP LLPNNVRDAL AGESTRPRVS RLGEGTLIT LRCINGSTDE RPDQLVAMRV YMDGRLIVST RQRKVLALDD VVSDLEEGTG PTDCGGWLVD VCDALTDHSS E FIEQLHDK IIDLEDNLLD QQIPPRGFLA LLRKQLIVMR RYMAPQRDVY ARLASERLPW MSDDQRRRMQ DIADRLGRGL DE IDACIAR TGVMADEIAQ VMQENLARRT YTMSLMAMVF LPSTFLTGLF GVNLGGIPGG GWQFGFSIFC ILLVVLIGGV ALW LHRSKW L

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333490
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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