8GHT | pdb_00008ght

Cryo-electron microscopy structure of the zinc transporter from Bordetella bronchiseptica

PDB DOI: https://doi.org/10.2210/pdb8GHT/pdb
EM Map EMD-40050: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Bordetella bronchiseptica
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2023-03-12 Released: 2023-06-21
Deposition Author(s): Liu, Q., Chai, J., Pang, C.X., Shanklin, J.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 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 mechanism of intracellular autoregulation of zinc uptake in ZIP transporters.

Pang, C., Chai, J., Zhu, P., Shanklin, J., Liu, Q.

(2023) Nat Commun 14: 3404-3404

PubMed: 37296139 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-39010-6
Primary Citation Related Structures:
8GHT

PubMed Abstract:
Zinc is an essential micronutrient that supports all living organisms through regulating numerous biological processes. However, the mechanism of uptake regulation by intracellular Zn ²⁺ status remains unclear. Here we report a cryo-electron microscopy structure of a ZIP-family transporter from Bordetella bronchiseptica at 3.05 Å resolution in an inward-facing, inhibited conformation. The transporter forms a homodimer, each protomer containing nine transmembrane helices and three metal ions. Two metal ions form a binuclear pore structure, and the third ion is located at an egress site facing the cytoplasm. The egress site is covered by a loop, and two histidine residues on the loop interact with the egress-site ion and regulate its release. Cell-based Zn ²⁺ uptake and cell growth viability assays reveal a negative regulation of Zn ²⁺ uptake through sensing intracellular Zn ²⁺ status using a built-in sensor. These structural and biochemical analyses provide mechanistic insight into the autoregulation of zinc uptake across membranes.

Organizational Affiliation

Biology Department, Brookhaven National Laboratory, Upton, NY, USA.

Macromolecule Content

Total Structure Weight: 64.73 kDa
Atom Count: 4,366
Modeled Residue Count: 608
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative membrane protein	A, B	312	Bordetella bronchiseptica	Mutation(s): 0 Gene Names: BB2405 Membrane Entity: Yes
UniProt
Find proteins for A0A0H3LM39 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LM39 Go to UniProtKB: A0A0H3LM39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3LM39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	F [auth A], G [auth B]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
CD (Subject of Investigation/LOI) Query on CD Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]