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Structure paper

TitleStructural titration reveals Ca-dependent conformational landscape of the IP receptor.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 6897, Year 2023
Publish dateOct 28, 2023
AuthorsNavid Paknejad / Vinay Sapuru / Richard K Hite /
PubMed AbstractInositol 1,4,5-trisphosphate receptors (IPRs) are endoplasmic reticulum Ca channels whose biphasic dependence on cytosolic Ca gives rise to Ca oscillations that regulate fertilization, cell division ...Inositol 1,4,5-trisphosphate receptors (IPRs) are endoplasmic reticulum Ca channels whose biphasic dependence on cytosolic Ca gives rise to Ca oscillations that regulate fertilization, cell division and cell death. Despite the critical roles of IPR-mediated Ca responses, the structural underpinnings of the biphasic Ca dependence that underlies Ca oscillations are incompletely understood. Here, we collect cryo-EM images of an IPR with Ca concentrations spanning five orders of magnitude. Unbiased image analysis reveals that Ca binding does not explicitly induce conformational changes but rather biases a complex conformational landscape consisting of resting, preactivated, activated, and inhibited states. Using particle counts as a proxy for relative conformational free energy, we demonstrate that Ca binding at a high-affinity site allows IPRs to activate by escaping a low-energy resting state through an ensemble of preactivated states. At high Ca concentrations, IPRs preferentially enter an inhibited state stabilized by a second, low-affinity Ca binding site. Together, these studies provide a mechanistic basis for the biphasic Ca-dependence of IPR channel activity.
External linksNat Commun / PubMed:37898605 / PubMed Central
MethodsEM (single particle)
Resolution2.5 - 5.55 Å
Structure data

EMDB-41323, PDB-8tk8:
Human Type 3 IP3 Receptor - Resting State (+IP3/ATP)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-41324: Human Type 3 IP3 Receptor - 3:1 Resting-to-Preactivated Transition State
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-41325: Human Type 3 IP3 Receptor - 2:2 Resting-to-Preactivated Transition State
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-41326: Human Type 3 IP3 Receptor - 1:3 Resting-to-Preactivated Transition State
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-41327: Human Type 3 IP3 Receptor - ARM2 Retraction Figure 4B
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-41328: Human Type 3 IP3 Receptor - ARM2 Retraction Figure 4C
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-41329: Human Type 3 IP3 Receptor - ARM2 Retraction Figure 4D
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-41330: Human Type 3 IP3 Receptor - ARM2 Retraction Figure 4E
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-41331: Human Type 3 IP3 Receptor - ARM2 Retraction Figure 4F
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-41332: Human Type 3 IP3 Receptor - ARM2 Retraction Figure 4G
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-41333: Human Type 3 IP3 Receptor - Wedge Loop Melting Progression Figure S15N
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-41334: Human Type 3 IP3 Receptor - Wedge Loop Melting Progression Figure S15I
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-41335: Human Type 3 IP3 Receptor - Wedge Loop Melting Progression Figure S15K
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-41336: Human Type 3 IP3 Receptor - Wedge Loop Melting Progression Figure S15M
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-41337: Human Type 3 IP3 Receptor - Wedge Loop Melting Progression Figure S15L
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-41338: Human Type 3 IP3 Receptor - Wedge Loop Melting Progression Figure S15J
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-41339: Human Type 3 IP3 Receptor - C2 Preactivated TMD Transitions (Figure 6D)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-41340: Human Type 3 IP3 Receptor - C4 Preactivated TMD Transitions (Figure 6E)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-41341: Human Type 3 IP3 Receptor - Activated CTD Frame 1 (Figure S18B)
Method: EM (single particle) / Resolution: 5.25 Å

EMDB-41342: Human Type 3 IP3 Receptor - Activated CTD Frame 2 (Figure S18B)
Method: EM (single particle) / Resolution: 5.22 Å

EMDB-41343: Human Type 3 IP3 Receptor - Activated CTD Frame 3 (Figure S18B)
Method: EM (single particle) / Resolution: 5.55 Å

EMDB-41344: Human Type 3 IP3 Receptor - C2 Resting TMD Transitions (Figure S8D)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-41345: Human Type 3 IP3 Receptor - C4 Resting TMD Transitions (Figure S8E)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-41347, PDB-8tkd:
Human Type 3 IP3 Receptor - Preactivated State (+IP3/ATP)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-41348, PDB-8tke:
Human Type 3 IP3 Receptor - Preactivated+Ca2+ State (+IP3/ATP/JD Ca2+)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-41349, PDB-8tkf:
Human Type 3 IP3 Receptor - Activated State (+IP3/ATP/JD Ca2+)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-41350, PDB-8tkg:
Human Type 3 IP3 Receptor - Resting State (+IP3/ATP)
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-41351, PDB-8tkh:
Human Type 3 IP3 Receptor - Labile Resting State 1 (+IP3/ATP)
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-41352, PDB-8tki:
Human Type 3 IP3 Receptor - Labile Resting State 2 (+IP3/ATP)
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-41365, PDB-8tl9:
Human Type 3 IP3 Receptor - Resting State (+IP3/ATP)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-41366, PDB-8tla:
Human Type 3 IP3 Receptor - Higher-Order Inhibited State - Symmetry Mate 1
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-ZN:
Unknown entry

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

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

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

ChemComp-CA:
Unknown entry

ChemComp-PT5:
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho / phospholipid*YM

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / Ion Channel / Calcium Channel / Endoplasmic Reticulum

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