8XMA | pdb_00008xma

Cryo-EM structure of human ZnT1 WT, in the presence of zinc, determined in an outward-facing conformation

PDB DOI: https://doi.org/10.2210/pdb8XMA/pdb
EM Map EMD-38469: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2023-12-27 Released: 2024-10-30
Deposition Author(s): Qu, Q., Long, Y., Zhou, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into human zinc transporter ZnT1 mediated Zn 2+ efflux.

Long, Y., Zhu, Z., Zhou, Z., Yang, C., Chao, Y., Wang, Y., Zhou, Q., Wang, M.W., Qu, Q.

(2024) EMBO Rep 25: 5006-5025

PubMed: 39390258 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44319-024-00287-3
Primary Citation Related Structures:
8XM6, 8XMA, 8XMF, 8XMJ, 8XN1

PubMed 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 in the structural characterization of various zinc transporters, the mechanism by which ZnTs-mediated Zn ²⁺ translocation is coupled with H ⁺ or Ca ²⁺ 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 ²⁺ ions coordinated at the TMD binding site by distinct compositions. At pH 6.0, ZnT1 complexed with Zn ²⁺ 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.

Organizational Affiliation

Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China.

Macromolecule Content

Total Structure Weight: 120.59 kDa
Atom Count: 4,858
Modeled Residue Count: 601
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton-coupled zinc antiporter SLC30A1	A [auth B], B [auth A]	530	Homo sapiens	Mutation(s): 0 Gene Names: SLC30A1, ZNT1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M5 (Homo sapiens) Explore Q9Y6M5 Go to UniProtKB: Q9Y6M5
PHAROS: Q9Y6M5 GTEx: ENSG00000170385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6M5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV0 Query on AV0 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain O [auth A] MOL2 format, chain G [auth B] MOL2 format, chain O [auth A] mmCIF format, chain G [auth B] mmCIF format, chain O [auth A]	G [auth B], O [auth A]	Lauryl Maltose Neopentyl Glycol C₄₇ H₈₈ O₂₂ MADJBYLAYPCCOO-VWHTXWAPSA-N		Interactions Focus chain G [auth B] Focus chain O [auth A] Interactions & Density Focus chain G [auth B] Focus chain O [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain P [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain P [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain P [auth A]	H [auth B], I [auth B], J [auth B], P [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth A] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	C [auth B] D [auth B] E [auth B] F [auth B] K [auth A] C [auth B], D [auth B], E [auth B], F [auth B], K [auth A], L [auth A], M [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]