8J1M

Crystal structure of a crosslinked variant of BbZIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular insights into substrate translocation in an elevator-type metal transporter.

Zhang, Y.Jafari, M.Zhang, T.Sui, D.Sagresti, L.Merz Jr., K.M.Hu, J.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.09.18.613805
  • Primary Citation of Related Structures:  
    8J1M

  • PubMed Abstract: 

    The Zrt/Irt-like protein (ZIP) metal transporters are key players in maintaining the homeostasis of a panel of essential microelements. The prototypical ZIP from Bordetella bronchiseptica (BbZIP) is an elevator transporter, but how the metal substrate moves along the transport pathway and how the transporter changes conformation to allow alternating access remain to be elucidated. Here, we combined structural, biochemical, and computational approaches to investigate the process of metal substrate translocation along with the global structural rearrangement. Our study revealed an upward hinge motion of the transport domain in a high-resolution crystal structure of a cross-linked variant, elucidated the mechanisms of metal release from the transport site into the cytoplasm and activity regulation by a cytoplasmic metal-binding loop, and unraveled an unusual elevator mode in enhanced sampling simulations that distinguishes BbZIP from other elevator transporters. This work provides important insights into the metal transport mechanism of the ZIP family.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Michigan State University, MI 48824.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative membrane protein289Bordetella bronchiseptica RB50Mutation(s): 2 
Gene Names: BB2405
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPG
Query on MPG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
HG (Subject of Investigation/LOI)
Query on HG

Download Ideal Coordinates CCD File 
L [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
CD (Subject of Investigation/LOI)
Query on CD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.407α = 90
b = 51.012β = 113.92
c = 51.817γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM140931
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115373

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release