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- PDB-8j7y: Cryo-EM structure of hZnT7DeltaHis-loop-Fab complex in zinc-bound... -

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Basic information

Entry
Database: PDB / ID: 8j7y
TitleCryo-EM structure of hZnT7DeltaHis-loop-Fab complex in zinc-bound state, determined in outward-facing conformation
Components
  • Heavy chain of YN7114-08 Fab
  • Light chain of YN7114-08 Fab
  • Zinc transporter 7Zinc transporter protein
KeywordsMETAL TRANSPORT / zinc / proton / transporter / Golgi apparatus / metal transporter / histidine-rich loop
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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHan, B.B. / Inaba, K. / Watanabe, S.
Funding support Japan, 3items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc transporter 7
E: Heavy chain of YN7114-08 Fab
C: Light chain of YN7114-08 Fab
F: Heavy chain of YN7114-08 Fab
B: Zinc transporter 7
D: Light chain of YN7114-08 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,3698
Polymers184,2386
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Zinc transporter 7 / Zinc transporter protein / ZnT-7 / Solute carrier family 30 member 7 / Znt-like transporter 2


Mass: 43004.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A7, ZNT7, ZNTL2 / Production host: Homo sapiens (human) / References: UniProt: Q8NEW0
#2: Antibody Heavy chain of YN7114-08 Fab


Mass: 24974.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Light chain of YN7114-08 Fab


Mass: 24140.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Human ZnT7Delta-His-loop-Fab complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142624 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211268
ELECTRON MICROSCOPYf_angle_d0.51515342
ELECTRON MICROSCOPYf_dihedral_angle_d3.3251520
ELECTRON MICROSCOPYf_chiral_restr0.041766
ELECTRON MICROSCOPYf_plane_restr0.0031938

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