[English] 日本語
Yorodumi
- EMDB-40050: Cryo-electron microscopy structure of the zinc transporter from B... -

+
Open data


ID or keywords:

Loading...

-
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 / zinc ion transmembrane transporter activity / 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 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40050.png

Downloads & links

-
Map

FileDownload / File: emd_40050.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 128 pix.
= 170.496 Å		1.33 Å/pix.
x 128 pix.
= 170.496 Å		1.33 Å/pix.
x 128 pix.
= 170.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.332 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Mask #1

Fileemd_40050_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40050_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_40050_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

UniProtKB: Zinc transporter ZIPB

-
Macromolecule #2: CADMIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

+
Image processing

Startup modelType of model: NONE
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more