[English] 日本語
Yorodumi
- EMDB-36051: Cryo-EM structure of hZnT7-Fab complex in zinc state 2, determine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36051
TitleCryo-EM structure of hZnT7-Fab complex in zinc state 2, determined in heterogeneous conformations- one subunit in an inward-facing zinc-bound and the other in an outward-facing zinc-bound conformation
Map data
Sample
  • Complex: Human ZnT7-Fab complex
    • Protein or peptide: Zinc transporter 7
    • Protein or peptide: Light chain of YN7114-08 Fab
    • Protein or peptide: Heavy chain of YN7114-08 Fab
  • Ligand: ZINC ION
Keywordszinc / proton / transporter / Golgi apparatus / metal transporter / histidine-rich loop / METAL TRANSPORT
Function / homology
Function and homology information


zinc ion import into Golgi lumen / Golgi cis cisterna membrane / zinc ion transmembrane transporter activity / intracellular zinc ion homeostasis / sarcoplasmic reticulum membrane / cytoplasmic vesicle / vesicle / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus ...zinc ion import into Golgi lumen / Golgi cis cisterna membrane / zinc ion transmembrane transporter activity / intracellular zinc ion homeostasis / sarcoplasmic reticulum membrane / cytoplasmic vesicle / vesicle / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
Zinc transporter Msc2-like / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsHan BB / Inaba K / Watanabe S
Funding support Japan, 3 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H03978 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H04758 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H05247 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn uptake into the Golgi apparatus.
Authors: Han Ba Bui / Satoshi Watanabe / Norimichi Nomura / Kehong Liu / Tomoko Uemura / Michio Inoue / Akihisa Tsutsumi / Hiroyuki Fujita / Kengo Kinoshita / Yukinari Kato / So Iwata / Masahide Kikkawa / Kenji Inaba /
Abstract: Zinc ions (Zn) are vital to most cells, with the intracellular concentrations of Zn being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein ...Zinc ions (Zn) are vital to most cells, with the intracellular concentrations of Zn being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein present the 2.2-3.1 Å-resolution cryo-EM structures of a Golgi-localized human Zn/H antiporter ZnT7 (hZnT7) in Zn-bound and unbound forms. Cryo-EM analyses show that hZnT7 exists as a dimer via tight interactions in both the cytosolic and transmembrane (TM) domains of two protomers, each of which contains a single Zn-binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn entry in the inward-facing conformation and widens the luminal cavity for Zn release in the outward-facing conformation. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 binds two Zn ions, seemingly facilitating Zn recruitment to the TM metal transport pathway. These structures permit mechanisms of hZnT7-mediated Zn uptake into the Golgi to be proposed.
History
DepositionApr 28, 2023-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36051.png

Downloads & links

-
Map

FileDownload / File: emd_36051.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 216 pix.
= 170.208 Å		0.79 Å/pix.
x 216 pix.
= 170.208 Å		0.79 Å/pix.
x 216 pix.
= 170.208 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.218
Minimum - Maximum-1.8376336 - 2.8415477
Average (Standard dev.)0.012530446 (±0.07576287)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin979797
Dimensions216216216
Spacing216216216
CellA=B=C: 170.208 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_36051_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_36051_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36051_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36051_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human ZnT7-Fab complex

EntireName: Human ZnT7-Fab complex
Components
  • Complex: Human ZnT7-Fab complex
    • Protein or peptide: Zinc transporter 7
    • Protein or peptide: Light chain of YN7114-08 Fab
    • Protein or peptide: Heavy chain of YN7114-08 Fab
  • Ligand: ZINC ION

-
Supramolecule #1: Human ZnT7-Fab complex

SupramoleculeName: Human ZnT7-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Zinc transporter 7

MacromoleculeName: Zinc transporter 7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.00432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGVAMPGAE DDVVMLPLSI KDDEYKPPKF NLFGKISGWF RSILSDKTSR NLFFFLCLNL SFAFVELLYG IWSNCLGLIS DSFHMFFDS TAILAGLAAS VISKWRDNDA FSYGYVRAEV LAGFVNGLFL IFTAFFIFSE GVERALAPPD VHHERLLLVS I LGFVVNLI ...String:
MGGVAMPGAE DDVVMLPLSI KDDEYKPPKF NLFGKISGWF RSILSDKTSR NLFFFLCLNL SFAFVELLYG IWSNCLGLIS DSFHMFFDS TAILAGLAAS VISKWRDNDA FSYGYVRAEV LAGFVNGLFL IFTAFFIFSE GVERALAPPD VHHERLLLVS I LGFVVNLI GIFVFKHGGH GHSHGSGHGH SHSLFNGALD QAHGHVDHCH SHEVKHGAAH SHDHAHGHGH FHSHDGPSLK ET TGPSRQI LQGVFLHILA DTLGSIGVIA SAIMMQNFGL MIADPICSIL IAILIVVSVI PLLRESVGIL MQRTPPLLEN SLP QCYQRV QQLQGVYSLQ EQHFWTLCSD VYVGTLKLIV APDADARWIL SQTHNIFTQA GVRQLYVQID FAAM

UniProtKB: Zinc transporter 7

-
Macromolecule #2: Light chain of YN7114-08 Fab

MacromoleculeName: Light chain of YN7114-08 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.140529 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVLTQSPAS LAVSLRRRAT ISCRASESVD GYGHSFMHWY QQKSGQPPKL LIYRASNLES GVPARFSGSG SRTDFTLTID PVEADDAAT YYCQQSNEDP YTFGSGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVLTQSPAS LAVSLRRRAT ISCRASESVD GYGHSFMHWY QQKSGQPPKL LIYRASNLES GVPARFSGSG SRTDFTLTID PVEADDAAT YYCQQSNEDP YTFGSGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

-
Macromolecule #3: Heavy chain of YN7114-08 Fab

MacromoleculeName: Heavy chain of YN7114-08 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.974102 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVQLQESGPG LVAPSQSLSI TCTVSGFSLT NYAVHWVRQS PGKGLEWLGV IWSNGRTDYN AAFISRLSIS KDNSKSQVFF KMNSLQADD TAIYYCARKL AYEGAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV ...String:
EVQLQESGPG LVAPSQSLSI TCTVSGFSLT NYAVHWVRQS PGKGLEWLGV IWSNGRTDYN AAFISRLSIS KDNSKSQVFF KMNSLQADD TAIYYCARKL AYEGAMDYWG QGTSVTVSSA KTTPPSVYPL APGSAAQTNS MVTLGCLVKG YFPEPVTVTW N SGSLSSGV HTFPAVLQSD LYTLSSSVTV PSSTWPSETV TCNVAHPASS TKVDKKIVPR DCGCKPCICT VPEVSS

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98881
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
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