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TitleConformational motions and ligand-binding underlying gating and regulation in IPR channel.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 6942, Year 2022
Publish dateNov 14, 2022
AuthorsGuizhen Fan / Mariah R Baker / Lara E Terry / Vikas Arige / Muyuan Chen / Alexander B Seryshev / Matthew L Baker / Steven J Ludtke / David I Yule / Irina I Serysheva /
PubMed AbstractInositol-1,4,5-trisphosphate receptors (IPRs) are activated by IP and Ca and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single ...Inositol-1,4,5-trisphosphate receptors (IPRs) are activated by IP and Ca and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IPR1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP, Ca and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IPR channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
External linksNat Commun / PubMed:36376291 / PubMed Central
MethodsEM (single particle)
Resolution3.26 - 3.5 Å
Structure data

27982

8eaq

EMDB-27982, PDB-8eaq:
Structure of the full-length IP3R1 channel determined at high Ca2+
Method: EM (single particle) / Resolution: 3.26 Å

27983

8ear

EMDB-27983, PDB-8ear:
Structure of the full-length IP3R1 channel determined in the presence of Calcium/IP3/ATP
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-PLX:
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL / phospholipid*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-I3P:
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate

Source
  • rattus norvegicus (Norway rat)
  • Norway rat (Norway rat)
KeywordsMEMBRANE PROTEIN / Calcium channel / lipid nanodisc

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