8CZJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

Starting Model: experimental
View more details

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

  • DOI: https://doi.org/10.1038/s41467-023-36048-4
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative membrane protein
A, B
309Bordetella bronchiseptica RB50Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3LM39
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPG (Subject of Investigation/LOI)
Query on MPG

Download Ideal Coordinates CCD File 
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
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.985α = 90
b = 117.661β = 104.16
c = 64.29γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Database references