6O84

Cryo-EM structure of OTOP3 from xenopus tropicalis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional characterization of an otopetrin family proton channel.

Chen, Q.Zeng, W.She, J.Bai, X.Jiang, Y.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.46710
  • Primary Citation of Related Structures:  
    6O84

  • PubMed Abstract: 

    The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from Xenopus tropicalis (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an α-helical barrel that could potentially serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residues - Gln 232/585 -Asp 262 /Asn 623 -Tyr 322/666 (the constriction triads). Mutagenesis shows that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. We also identified several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels.


  • Organizational Affiliation

    Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LOC100127796 protein,LOC100127796 protein,OTOP3,LOC100127796 protein,LOC100127796 protein
A, B
690Xenopus tropicalisMutation(s): 0 
Gene Names: otop3LOC100127796
Membrane Entity: Yes 
UniProt
Find proteins for A9JTM7 (Xenopus tropicalis)
Explore A9JTM7 
Go to UniProtKB:  A9JTM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9JTM7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesGM079179
Howard Hughes Medical Institute (HHMI)United States--
Other privateUnited Statesthe Cancer Prevention and Research Initiative of Texas
Other privateUnited StatesMurchison Linthicum Scholar in Medical Research fund
Welch FoundationUnited StatesI-1578

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references