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- EMDB-38474: Cryo-EM structure of human ZnT1 WT at a low PH, in the presence o... -

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Basic information

Entry
Database: EMDB / ID: EMD-38474
TitleCryo-EM structure of human ZnT1 WT at a low PH, in the presence of zinc, determined in an outward-facing conformation.
Map data
Sample
  • Complex: Zinc transporter 1
    • Protein or peptide: Human zinc transpoter 1
KeywordsHuman ZnT1 / Zinc transpoter / outward-facing conformation / transport protein. / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQu Q / Long Y / Zhou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: EMBO Rep / Year: 2024
Title: Structural insights into human zinc transporter ZnT1 mediated Zn efflux.
Authors: Yonghui Long / Zhini Zhu / Zixuan Zhou / Chuanhui Yang / Yulin Chao / Yuwei Wang / Qingtong Zhou / Ming-Wei Wang / Qianhui Qu /
Abstract: Zinc transporter 1 (ZnT1), the principal carrier of cytosolic zinc to the extracellular milieu, is important for cellular zinc homeostasis and resistance to zinc toxicity. Despite recent advancements ...Zinc transporter 1 (ZnT1), the principal carrier of cytosolic zinc to the extracellular milieu, is important for cellular zinc homeostasis and resistance to zinc toxicity. Despite recent advancements in the structural characterization of various zinc transporters, the mechanism by which ZnTs-mediated Zn translocation is coupled with H or Ca remains unclear. To visualize the transport dynamics, we determined the cryo-electron microscopy (cryo-EM) structures of human ZnT1 at different functional states. ZnT1 dimerizes via extensive interactions between the cytosolic (CTD), the transmembrane (TMD), and the unique cysteine-rich extracellular (ECD) domains. At pH 7.5, both protomers adopt an outward-facing (OF) conformation, with Zn ions coordinated at the TMD binding site by distinct compositions. At pH 6.0, ZnT1 complexed with Zn exhibits various conformations [OF/OF, OF/IF (inward-facing), and IF/IF]. These conformational snapshots, together with biochemical investigation and molecular dynamic simulations, shed light on the mechanism underlying the proton-dependence of ZnT1 transport.
History
DepositionDec 27, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38474.png

Downloads & links

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Map

FileDownload / File: emd_38474.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 260 pix.
= 216.32 Å		0.83 Å/pix.
x 260 pix.
= 216.32 Å		0.83 Å/pix.
x 260 pix.
= 216.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-1.5317199 - 2.0614955
Average (Standard dev.)-0.00015114745 (±0.055761687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 216.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38474_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_38474_half_map_2.map
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Sample components

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Entire : Zinc transporter 1

EntireName: Zinc transporter 1
Components
  • Complex: Zinc transporter 1
    • Protein or peptide: Human zinc transpoter 1

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Supramolecule #1: Zinc transporter 1

SupramoleculeName: Zinc transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Human zinc transpoter 1

MacromoleculeName: Human zinc transpoter 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGCWGRNRGR LLCMLALTFM FMVLEVVVSR VTSSLAMLSD SFHMLSDVLA LVVALVAERF ARRTHATQKN TFGWIRAEVM GALVNAIFLT GLCFAILLEA IERFIEPHEM QQPLVVLGVG VAGLLVNVLG LCLFHHHSGF SQDSGHGHSH GGHGHGHGLP KGPRVKSTRP ...String:
MGCWGRNRGR LLCMLALTFM FMVLEVVVSR VTSSLAMLSD SFHMLSDVLA LVVALVAERF ARRTHATQKN TFGWIRAEVM GALVNAIFLT GLCFAILLEA IERFIEPHEM QQPLVVLGVG VAGLLVNVLG LCLFHHHSGF SQDSGHGHSH GGHGHGHGLP KGPRVKSTRP GSSDINVAPG EQGPDQEETN TLVANTSNSN GLKLDPADPE NPRSGDTVEV QVNGNLVREP DHMELEEDRA GQLNMRGVFL HVLGDALGSV IVVVNALVFY FSWKGCSEGD FCVNPCFPDP CKAFVEIINS THASVYEAGP CWVLYLDPTL CVVMVCILLY TTYPLLKESA LILLQTVPKQ IDIRNLIKEL RNVEGVEEVH ELHVWQLAGS RIIATAHIKC EDPTSYMEVA KTIKDVFHNH GIHATTIQPE FASVGSKSSV VPCELACRTQ CALKQCCGTL PQAPSGKDAE KTPAVSISCL ELSNNLEKKP RRTKAENIPA VVIEIKNMPN KQPESSLSDL EVLFQGPEFS RLEEELRRRT EPGSENLYFQ

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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: 6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 260.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97184
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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