6O84

Cryo-EM structure of OTOP3 from xenopus tropicalis

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Xenopus tropicalis
  • Expression System: Homo sapiens

  • Deposited: 2019-03-08 Released: 2019-04-24 
  • Deposition Author(s): Chen, Q.F., Bai, X.C., Jiang, Y.X.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR); Howard Hughes Medical Institute (HHMI); Other private; Welch Foundation 

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 1.2 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: 10.7554/eLife.46710

  • PubMed Abstract: 
  • The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from <i>Xenopus tropicalis </i> (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer w ...

    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.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LOC100127796 protein,LOC100127796 protein,OTOP3,LOC100127796 protein,LOC100127796 protein
A, B
690Xenopus tropicalisMutation(s): 0 
Gene Names: otop3 (engase, fbxo28, LOC100127796)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Other Ion Channels
Protein: 
OTOP3 otopetrin proton channel
Find proteins for A9JTM7 (Xenopus tropicalis)
Go to UniProtKB:  A9JTM7
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Author supporting evidence
  • Version 1.2: 2019-12-18
    Type: Other