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Article ; Online: Structural insights into gap junction channels boosted by cryo-EM.

Oshima, Atsunori

2020 Volume 63, Page(s) 42–48

Abstract: Regulating intercellular communication is essential for multicellular organisms. Gap junction channels are the major components mediating this function, but the molecular mechanisms underlying their opening and closing remain unclear. Single-particle ... ...

Abstract	Regulating intercellular communication is essential for multicellular organisms. Gap junction channels are the major components mediating this function, but the molecular mechanisms underlying their opening and closing remain unclear. Single-particle cryo-electron microscopy (cryo-EM) is a powerful tool for investigating high-resolution protein structures that are difficult to crystallize, such as gap junction channels. Membrane protein structures are often determined in a detergent solubilized form, but lipid bilayers provide a near native environment for structural analysis. This review focuses on recent reports of gap junction channel structures visualized by cryo-EM. An overview of the differences observed in gap junction channel structures in the presence and absence of lipids is described, which may contribute to elucidating the regulation mechanisms of gap junction channel function.
MeSH term(s)	Animals ; Connexins/chemistry ; Connexins/metabolism ; Cryoelectron Microscopy ; Gap Junctions/chemistry ; Gap Junctions/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channels/chemistry ; Ion Channels/metabolism ; Models, Molecular ; Phospholipids/chemistry ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Structure-Activity Relationship
Chemical Substances	Connexins ; Ion Channels ; Phospholipids
Language	English
Publishing date	2020-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2020.03.008
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Article ; Online: Potential of cryo-EM for high-resolution structural analysis of gap junction channels.

Oshima, Atsunori

Current opinion in structural biology

2019 Volume 54, Page(s) 78–85

Abstract: Gap junction family proteins form conduits connecting the cytoplasm of adjacent cells, thereby enabling electrical and chemical coupling to maintain physiological homeostasis. Gap junction proteins comprise two gene families, connexins in chordates and ... ...

Abstract	Gap junction family proteins form conduits connecting the cytoplasm of adjacent cells, thereby enabling electrical and chemical coupling to maintain physiological homeostasis. Gap junction proteins comprise two gene families, connexins in chordates and innexins in pre-chordates. Their channel structures have been analyzed by electron or X-ray crystallography, but only a few atomic structures have been reported. Recent advances in single-particle cryo-electron microscopy (cryo-EM) will help to elucidate these structures further. Here the structural biology of gap junction channels utilizing crystallography and single-particle cryo-EM is overviewed to shed light on the functional mechanisms of cell-cell communication that are essential for multicellular organisms.
MeSH term(s)	Animals ; Connexins/chemistry ; Connexins/metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Gap Junctions/metabolism ; Humans
Chemical Substances	Connexins
Language	English
Publishing date	2019-02-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2019.01.005
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Article ; Online: Structure of an innexin gap junction channel and cryo-EM sample preparation.

Oshima, Atsunori

Microscopy (Oxford, England)

2017 Volume 66, Issue 6, Page(s) 371–379

Abstract: Gap junction channels are essential for mediating intercellular communication in most multicellular organisms. Two gene families encode gap junction channels, innexin and connexin. Although the sequence similarity between these two families based on ... ...

Abstract	Gap junction channels are essential for mediating intercellular communication in most multicellular organisms. Two gene families encode gap junction channels, innexin and connexin. Although the sequence similarity between these two families based on bioinformatics is not conclusively determined, the gap junction channels encoded by these two gene families are structurally and functionally analogous. We recently reported an atomic structure of an invertebrate innexin gap junction channel using single-particle cryo-electron microscopy. Our findings revealed that connexin and innexin families share several structural properties with regard to their monomeric and oligomeric structures, while simultaneously suggesting a diversity of gap junction channels in nature. This review summarizes cutting-edge progress toward determining an innexin gap junction channel structure, as well as essential tips for preparing cryo-electron microscopy samples for high-resolution structural analysis of an innexin gap junction channel.
MeSH term(s)	Animals ; Biological Transport ; Cell Communication ; Connexins/chemistry ; Connexins/ultrastructure ; Cryoelectron Microscopy/methods ; Gap Junctions/chemistry ; Gap Junctions/ultrastructure ; Specimen Handling/instrumentation ; Specimen Handling/methods
Chemical Substances	Connexins
Language	English
Publishing date	2017-10-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2707496-1
ISSN	2050-5701 ; 2050-5698
ISSN (online)	2050-5701
ISSN	2050-5698
DOI	10.1093/jmicro/dfx035
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Article ; Online: The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel.

Irie, Katsumasa / Oda, Yoshinori / Sumikama, Takashi / Oshima, Atsunori / Fujiyoshi, Yoshinori

Nature communications

2023 Volume 14, Issue 1, Page(s) 4236

Abstract: Divalent cation block is observed in various tetrameric ion channels. For blocking, a divalent cation is thought to bind in the ion pathway of the channel, but such block has not yet been directly observed. So, the behaviour of these blocking divalent ... ...

Abstract	Divalent cation block is observed in various tetrameric ion channels. For blocking, a divalent cation is thought to bind in the ion pathway of the channel, but such block has not yet been directly observed. So, the behaviour of these blocking divalent cations remains still uncertain. Here, we elucidated the mechanism of the divalent cation block by reproducing the blocking effect into NavAb, a well-studied tetrameric sodium channel. Our crystal structures of NavAb mutants show that the mutations increasing the hydrophilicity of the inner vestibule of the pore domain enable a divalent cation to stack on the ion pathway. Furthermore, non-equilibrium molecular dynamics simulation showed that the stacking calcium ion repel sodium ion at the bottom of the selectivity filter. These results suggest the primary process of the divalent cation block mechanism in tetrameric cation channels.
MeSH term(s)	Cations, Divalent/metabolism ; Sodium Channels/metabolism ; Ion Channels ; Cations/metabolism ; Mutation ; Calcium/metabolism
Chemical Substances	Cations, Divalent ; Sodium Channels ; Ion Channels ; Cations ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-07-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-39987-0
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Article ; Online: Structure and closure of connexin gap junction channels.

Oshima, Atsunori

FEBS letters

2014 Volume 588, Issue 8, Page(s) 1230–1237

Abstract: Connexin gap junctions comprise assembled channels penetrating two plasma membranes for which gating regulation is associated with a variety of factors, including voltage, pH, Ca(2+), and phosphorylation. Functional studies have established that various ... ...

Abstract	Connexin gap junctions comprise assembled channels penetrating two plasma membranes for which gating regulation is associated with a variety of factors, including voltage, pH, Ca(2+), and phosphorylation. Functional studies have established that various parts of the connexin peptides are related to channel closure and electrophysiology studies have provided several working models for channel gating. The corresponding structural models supporting these findings, however, are not sufficient because only small numbers of closed connexin structures have been reported. To fully understand the gating mechanisms, the channels should be visualized in both the open and closed states. Electron crystallography and X-ray crystallography studies recently revealed three-dimensional structures of connexin channels in a couple of states in which the main difference is the conformation of the N-terminal domain, which have helped to clarify the structure in regard to channel closure. Here the closure models for connexin gap junction channels inferred from structural and functional studies are described in the context of each domain of the connexin protein associated with gating modulation.
MeSH term(s)	Amino Acid Sequence ; Animals ; Connexins/chemistry ; Connexins/genetics ; Connexins/metabolism ; Humans ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Protein Conformation
Chemical Substances	Connexins
Language	English
Publishing date	2014-04-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2014.01.042
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Article ; Online: Structural basis of hydroxycarboxylic acid receptor signaling mechanisms through ligand binding.

Suzuki, Shota / Tanaka, Kotaro / Nishikawa, Kouki / Suzuki, Hiroshi / Oshima, Atsunori / Fujiyoshi, Yoshinori

Nature communications

2023 Volume 14, Issue 1, Page(s) 5899

Abstract: Hydroxycarboxylic acid receptors (HCA) are expressed in various tissues and immune cells. HCA2 and its agonist are thus important targets for treating inflammatory and metabolic disorders. Only limited information is available, however, on the active- ... ...

Abstract	Hydroxycarboxylic acid receptors (HCA) are expressed in various tissues and immune cells. HCA2 and its agonist are thus important targets for treating inflammatory and metabolic disorders. Only limited information is available, however, on the active-state binding of HCAs with agonists. Here, we present cryo-EM structures of human HCA2-Gi and HCA3-Gi signaling complexes binding with multiple compounds bound. Agonists were revealed to form a salt bridge with arginine, which is conserved in the HCA family, to activate these receptors. Extracellular regions of the receptors form a lid-like structure that covers the ligand-binding pocket. Although transmembrane (TM) 6 in HCAs undergoes dynamic conformational changes, ligands do not directly interact with amino acids in TM6, suggesting that indirect signaling induces a slight shift in TM6 to activate Gi proteins. Structural analyses of agonist-bound HCA2 and HCA3 together with mutagenesis and molecular dynamics simulation provide molecular insights into HCA ligand recognition and activation mechanisms.
MeSH term(s)	Humans ; Ligands ; Signal Transduction ; Amino Acids ; Amines ; Arginine
Chemical Substances	Ligands ; Amino Acids ; Amines ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2023-09-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-41650-7
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Article: Structure and closure of connexin gap junction channels

Oshima, Atsunori

Federation of European Biochemical Societies FEBS letters. 2014 Apr. 17, v. 588, no. 8

2014

Abstract: Connexin gap junctions comprise assembled channels penetrating two plasma membranes for which gating regulation is associated with a variety of factors, including voltage, pH, Ca2+, and phosphorylation. Functional studies have established that various ... ...

Abstract	Connexin gap junctions comprise assembled channels penetrating two plasma membranes for which gating regulation is associated with a variety of factors, including voltage, pH, Ca2+, and phosphorylation. Functional studies have established that various parts of the connexin peptides are related to channel closure and electrophysiology studies have provided several working models for channel gating. The corresponding structural models supporting these findings, however, are not sufficient because only small numbers of closed connexin structures have been reported. To fully understand the gating mechanisms, the channels should be visualized in both the open and closed states. Electron crystallography and X-ray crystallography studies recently revealed three-dimensional structures of connexin channels in a couple of states in which the main difference is the conformation of the N-terminal domain, which have helped to clarify the structure in regard to channel closure. Here the closure models for connexin gap junction channels inferred from structural and functional studies are described in the context of each domain of the connexin protein associated with gating modulation.
Keywords	X-ray diffraction ; calcium ; electrophysiology ; gap junctions ; models ; pH ; peptides ; phosphorylation ; plasma membrane
Language	English
Dates of publication	2014-0417
Size	p. 1230-1237.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2014.01.042
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Article ; Online: Cryo-EM of the ATP11C flippase reconstituted in Nanodiscs shows a distended phospholipid bilayer inner membrane around transmembrane helix 2.

Nakanishi, Hanayo / Hayashida, Kenichi / Nishizawa, Tomohiro / Oshima, Atsunori / Abe, Kazuhiro

The Journal of biological chemistry

2021 Volume 298, Issue 1, Page(s) 101498

Abstract: ATP11C is a member of the P4-ATPase flippase family that mediates translocation of phosphatidylserine (PtdSer) across the lipid bilayer. In order to characterize the structure and function of ATP11C in a model natural lipid environment, we revisited and ... ...

Abstract	ATP11C is a member of the P4-ATPase flippase family that mediates translocation of phosphatidylserine (PtdSer) across the lipid bilayer. In order to characterize the structure and function of ATP11C in a model natural lipid environment, we revisited and optimized a quick procedure for reconstituting ATP11C into Nanodiscs using methyl-β-cyclodextrin as a reagent for the detergent removal. ATP11C was efficiently reconstituted with the endogenous lipid, or the mixture of endogenous lipid and synthetic dioleoylphosphatidylcholine (DOPC)/dioleoylphosphatidylserine (DOPS), all of which retained the ATPase activity. We obtained 3.4 Å and 3.9 Å structures using single-particle cryo-electron microscopy (cryo-EM) of AlF- and BeF-stabilized ATP11C transport intermediates, respectively, in a bilayer containing DOPS. We show that the latter exhibited a distended inner membrane around ATP11C transmembrane helix 2, possibly reflecting the perturbation needed for phospholipid release to the lipid bilayer. Our structures of ATP11C in the lipid membrane indicate that the membrane boundary varies upon conformational changes of the enzyme and is no longer flat around the protein, a change that likely contributes to phospholipid translocation across the membrane leaflets.
MeSH term(s)	Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/metabolism ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cryoelectron Microscopy ; Lipid Bilayers/chemistry ; Lipid Bilayers/metabolism ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/metabolism ; Phospholipids/chemistry ; Phospholipids/metabolism
Chemical Substances	Lipid Bilayers ; Membrane Transport Proteins ; Phospholipids ; Adenosine Triphosphatases (EC 3.6.1.-)
Language	English
Publishing date	2021-12-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.101498
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Article ; Online: Gastric proton pump with two occluded K

Abe, Kazuhiro / Yamamoto, Kenta / Irie, Katsumasa / Nishizawa, Tomohiro / Oshima, Atsunori

Nature communications

2021 Volume 12, Issue 1, Page(s) 5709

Abstract: The gastric ... ...

Abstract	The gastric H
MeSH term(s)	Binding Sites/genetics ; Cations, Monovalent/metabolism ; Cell Membrane/enzymology ; Cryoelectron Microscopy ; Crystallization ; Enzyme Assays ; Gastric Mucosa/cytology ; Gastric Mucosa/enzymology ; H(+)-K(+)-Exchanging ATPase/genetics ; H(+)-K(+)-Exchanging ATPase/isolation & purification ; H(+)-K(+)-Exchanging ATPase/metabolism ; H(+)-K(+)-Exchanging ATPase/ultrastructure ; HEK293 Cells ; Humans ; Models, Molecular ; Mutation ; Potassium/metabolism ; Protein Engineering ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism ; Recombinant Proteins/ultrastructure ; Substrate Specificity/genetics
Chemical Substances	Cations, Monovalent ; Recombinant Proteins ; H(+)-K(+)-Exchanging ATPase (EC 3.6.3.10) ; Potassium (RWP5GA015D)
Language	English
Publishing date	2021-09-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-26024-1
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Article ; Online: Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM.

Suzuki, Shota / Iida, Momoko / Hiroaki, Yoko / Tanaka, Kotaro / Kawamoto, Akihiro / Kato, Takayuki / Oshima, Atsunori

Communications biology

2022 Volume 5, Issue 1, Page(s) 707

Abstract: MrgD, a member of the Mas-related G protein-coupled receptor (MRGPR) family, has high basal activity for Gi activation. It recognizes endogenous ligands, such as β-alanine, and is involved in pain and itch signaling. The lack of a high-resolution ... ...

Abstract	MrgD, a member of the Mas-related G protein-coupled receptor (MRGPR) family, has high basal activity for Gi activation. It recognizes endogenous ligands, such as β-alanine, and is involved in pain and itch signaling. The lack of a high-resolution structure for MrgD hinders our understanding of whether its activation is ligand-dependent or constitutive. Here, we report two cryo-EM structures of the MrgD-Gi complex in the β-alanine-bound and apo states at 3.1 Å and 2.8 Å resolution, respectively. These structures show that β-alanine is bound to a shallow pocket at the extracellular domains. The extracellular half of the sixth transmembrane helix undergoes a significant movement and is tightly packed into the third transmembrane helix through hydrophobic residues, creating the active form. Our structures demonstrate a structural basis for the characteristic ligand recognition of MrgD. These findings provide a framework to guide drug designs targeting the MrgD receptor.
MeSH term(s)	Cryoelectron Microscopy ; Ligands ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction ; beta-Alanine
Chemical Substances	Ligands ; Receptors, G-Protein-Coupled ; beta-Alanine (11P2JDE17B)
Language	English
Publishing date	2022-07-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03668-3
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