8XMA | pdb_00008xma

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


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

  • DOI: https://doi.org/10.1038/s44319-024-00287-3
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-coupled zinc antiporter SLC30A1A [auth B],
B [auth A]
530Homo sapiensMutation(s): 0 
Gene Names: SLC30A1ZNT1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6M5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AV0
Query on AV0

Download Ideal Coordinates CCD File 
G [auth B],
O [auth A]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-VWHTXWAPSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B],
J [auth B],
P [auth A]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171194

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references