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- EMDB-40050: Cryo-electron microscopy structure of the zinc transporter from B... -

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Basic information

Entry
Database: EMDB / ID: EMD-40050
TitleCryo-electron microscopy structure of the zinc transporter from Bordetella bronchiseptica
Map data
Sample
  • Complex: Zinc transporter dimer from Bordetella bronchiseptica
    • Protein or peptide: Putative membrane protein
  • Ligand: CADMIUM ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
Keywordszinc transporter / dimer / complex / metal binding / inward-open inhibited conformation / TRANSPORT PROTEIN
Function / homologyZinc/iron permease / ZIP Zinc transporter / metal ion transmembrane transporter activity / zinc ion transport / plasma membrane / Zinc transporter ZIPB
Function and homology information
Biological speciesBordetella bronchiseptica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsLiu Q / Chai J / Pang CX / Shanklin J
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural mechanism of intracellular autoregulation of zinc uptake in ZIP transporters.
Authors: Changxu Pang / Jin Chai / Ping Zhu / John Shanklin / Qun Liu /
Abstract: Zinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn status remains ...Zinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn status remains unclear. Here we report a cryo-electron microscopy structure of a ZIP-family transporter from Bordetella bronchiseptica at 3.05 Å resolution in an inward-facing, inhibited conformation. The transporter forms a homodimer, each protomer containing nine transmembrane helices and three metal ions. Two metal ions form a binuclear pore structure, and the third ion is located at an egress site facing the cytoplasm. The egress site is covered by a loop, and two histidine residues on the loop interact with the egress-site ion and regulate its release. Cell-based Zn uptake and cell growth viability assays reveal a negative regulation of Zn uptake through sensing intracellular Zn status using a built-in sensor. These structural and biochemical analyses provide mechanistic insight into the autoregulation of zinc uptake across membranes.
History
DepositionMar 12, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40050.png

Downloads & links

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Map

FileDownload / File: emd_40050.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.332 Å
Density
Contour LevelBy AUTHOR: 0.338
Minimum - Maximum-0.6583064 - 1.9811351
Average (Standard dev.)0.013746325 (±0.09061749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 170.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40050_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40050_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40050_half_map_2.map
Projections & Slices
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Sample components

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Entire : Zinc transporter dimer from Bordetella bronchiseptica

EntireName: Zinc transporter dimer from Bordetella bronchiseptica
Components
  • Complex: Zinc transporter dimer from Bordetella bronchiseptica
    • Protein or peptide: Putative membrane protein
  • Ligand: CADMIUM ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: Zinc transporter dimer from Bordetella bronchiseptica

SupramoleculeName: Zinc transporter dimer from Bordetella bronchiseptica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bordetella bronchiseptica (bacteria)

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Macromolecule #1: Putative membrane protein

MacromoleculeName: Putative membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bordetella bronchiseptica (bacteria)
Molecular weightTheoretical: 31.291566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMNQPSSL AADLRGAWHA QAQSHPLITL GLAASAAGVV LLLVAGIVNA LTGENRVHVG YAVLGGAAGF AATALGALMA LGLRAISAR TQDAMLGFAA GMMLAASAFS LILPGLDAAG TIVGPGPAAA AVVALGLGLG VLLMLGLDYF TPHEHERTGH Q GPEAARVN ...String:
GSHMNQPSSL AADLRGAWHA QAQSHPLITL GLAASAAGVV LLLVAGIVNA LTGENRVHVG YAVLGGAAGF AATALGALMA LGLRAISAR TQDAMLGFAA GMMLAASAFS LILPGLDAAG TIVGPGPAAA AVVALGLGLG VLLMLGLDYF TPHEHERTGH Q GPEAARVN RVWLFVLTII LHNLPEGMAI GVSFATGDLR IGLPLTSAIA IQDVPEGLAV ALALRAVGLP IGRAVLVAVA SG LMEPLGA LVGVGISSGF ALAYPISMGL AAGAMIFVVS HEVIPETHRN GHETTATVGL MAGFALMMFL DTALG

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Macromolecule #2: CADMIUM ION

MacromoleculeName: CADMIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CD
Molecular weightTheoretical: 112.411 Da

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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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

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37954
FSC plot (resolution estimation)

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