6IZ5 | pdb_00006iz5

Crystal Structure Analysis of a Eukaryotic Membrane Protein

• PDB DOI: https://doi.org/10.2210/pdb6IZ5/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Xenopus laevis
• Expression System: Schizosaccharomyces
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-12-18 Released: 2019-05-01 
• Deposition Author(s): Li, D., Su, M., Hendrickson, W.A., Chen, Y.H.
• Funding Organization(s): Ministry of Science and Technology (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.327 (Depositor), 0.334 (DCC) 
• R-Value Work: 
  0.311 (Depositor), 0.319 (DCC) 
• R-Value Observed: 
  0.312 (Depositor) 

Starting Model: experimental

Literature

Structural basis for activity of TRIC counter-ion channels in calcium release.

Wang, X.H., Su, M., Gao, F., Xie, W., Zeng, Y., Li, D.L., Liu, X.L., Zhao, H., Qin, L., Li, F., Liu, Q., Clarke, O.B., Lam, S.M., Shui, G.H., Hendrickson, W.A., Chen, Y.H.

(2019) Proc Natl Acad Sci U S A 116: 4238-4243

• PubMed: 30770441 
• DOI: https://doi.org/10.1073/pnas.1817271116
• Primary Citation Related Structures: 
  6IYU, 6IYX, 6IYZ, 6IZ0, 6IZ1, 6IZ3, 6IZ4, 6IZ5, 6IZ6, 6IZF


• PubMed Abstract: 
  

  Trimeric intracellular cation (TRIC) channels are thought to provide counter-ion currents that facilitate the active release of Ca ²⁺ from intracellular stores. TRIC activity is controlled by voltage and Ca ²⁺ modulation, but underlying mechanisms have remained unknown. Here we describe high-resolution crystal structures of vertebrate TRIC-A and TRIC-B channels, both in Ca ²⁺ -bound and Ca ²⁺ -free states, and we analyze conductance properties in structure-inspired mutagenesis experiments. The TRIC channels are symmetric trimers, wherein we find a pore in each protomer that is gated by a highly conserved lysine residue. In the resting state, Ca ²⁺ binding at the luminal surface of TRIC-A, on its threefold axis, stabilizes lysine blockage of the pores. During active Ca ²⁺ release, luminal Ca ²⁺ depletion removes inhibition to permit the lysine-bearing and voltage-sensing helix to move in response to consequent membrane hyperpolarization. Diacylglycerol is found at interprotomer interfaces, suggesting a role in metabolic control.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
CAS Center for Excellence in Biomacromolecules, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
Department of Biology, New York University, New York, NY 10003.
Biology Department, Brookhaven National Laboratory, Upton, NY 11793.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032; [e-mail] [e-mail].
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.
State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 35.46 kDa 
• Atom Count: 1,769 
• Modeled Residue Count: 224 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trimeric intracellular cation channel type B-B	A	314	Xenopus laevis	Mutation(s): 0  Gene Names: tmem38b-b Membrane Entity: Yes
UniProt
Find proteins for Q6GN30 (Xenopus laevis) Explore Q6GN30  Go to UniProtKB:  Q6GN30

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.327 (Depositor), 0.334 (DCC) 
• R-Value Work:  0.311 (Depositor), 0.319 (DCC) 
• R-Value Observed: 0.312 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.009	α = 90
b = 250.009	β = 90
c = 250.009	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Li, D., Su, M., Hendrickson, W.A., Chen, Y.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0500503
Ministry of Science and Technology (China)	China	2015CB910102

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description