8CZJ | pdb_00008czj

A bacteria Zrt/Irt-like protein in the apo state

PDB DOI: https://doi.org/10.2210/pdb8CZJ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bordetella bronchiseptica RB50
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2022-05-24 Released: 2023-02-22
Deposition Author(s): Zhang, Y., Hu, J.
Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.261 (Depositor), 0.246 (DCC)
R-Value Work:
0.233 (Depositor)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter.

Zhang, Y., Jiang, Y., Gao, K., Sui, D., Yu, P., Su, M., Wei, G.W., Hu, J.

(2023) Nat Commun 14: 385-385

PubMed: 36693843 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-36048-4
Primary Citation Related Structures:
8CZJ

PubMed Abstract:
The Zrt-/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent metal transporters critically involved in maintaining systemic and cellular homeostasis of zinc, iron, and manganese. Here, we present a study on a prokaryotic ZIP from Bordetella bronchiseptica (BbZIP) by combining structural biology, evolutionary covariance, computational modeling, and a variety of biochemical assays to tackle the issue of the transport mechanism which has not been established for the ZIP family. The apo state structure in an inward-facing conformation revealed a disassembled transport site, altered inter-helical interactions, and importantly, a rigid body movement of a 4-transmembrane helix (TM) bundle relative to the other TMs. The computationally generated and biochemically validated outward-facing conformation model revealed a slide of the 4-TM bundle, which carries the transport site(s), by approximately 8 Å toward the extracellular side against the static TMs which mediate dimerization. These findings allow us to conclude that BbZIP is an elevator-type transporter.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.

Macromolecule Content

Total Structure Weight: 66 kDa
Atom Count: 4,289
Modeled Residue Count: 591
Deposited Residue Count: 618
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	309	Bordetella bronchiseptica RB50	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
MPG (Subject of Investigation/LOI) Query on MPG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain N [auth B]	F [auth A] G [auth A] I [auth A] N [auth B] O [auth B] F [auth A], G [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	C [auth A] D [auth A] E [auth A] H [auth A] J [auth B] C [auth A], D [auth A], E [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]