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Structure paper

TitleStructural basis for the regulation of inositol trisphosphate receptors by Ca and IP.
Journal, issue, pagesNat Struct Mol Biol, Vol. 25, Issue 8, Page 660-668, Year 2018
Publish dateJul 16, 2018
AuthorsNavid Paknejad / Richard K Hite /
PubMed AbstractInositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, ...Inositol trisphosphate receptors (IPRs) are ubiquitous Ca-permeable channels that mediate release of Ca from the endoplasmic reticulum, thereby regulating numerous processes including cell division, cell death, differentiation and fertilization. IPRs are jointly activated by inositol trisphosphate (IP) and their permeant ion, Ca. At high concentrations, however, Ca inhibits activity, ensuring precise spatiotemporal control over intracellular Ca. Despite extensive characterization of IPR, the mechanisms through which these molecules control channel gating have remained elusive. Here, we present structures of full-length human type 3 IPRs in ligand-bound and ligand-free states. Multiple IP-bound structures demonstrate that the large cytoplasmic domain provides a platform for propagation of long-range conformational changes to the ion-conduction gate. Structures in the presence of Ca reveal two Ca-binding sites that induce the disruption of numerous interactions between subunits, thereby inhibiting IPR. These structures thus provide a mechanistic basis for beginning to understand the regulation of IPR.
External linksNat Struct Mol Biol / PubMed:30013099 / PubMed Central
MethodsEM (single particle)
Resolution3.26 - 6.01 Å
Structure data

EMDB-7978, PDB-6dqj:
Human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-7979:
Cytoplasmic domain of human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state
Method: EM (single particle) / Resolution: 3.69 Å

EMDB-7980:
Human type 3 1,4,5-inositol trisphosphate receptor in a ligand-free state
Method: EM (single particle) / Resolution: 3.69 Å

EMDB-7981, PDB-6dqn:
Class 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.33 Å

EMDB-7982:
Cytoplasmic domain of class 1 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-7983, PDB-6dqs:
Class 3 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 4.12 Å

EMDB-7984, PDB-6dqv:
Class 2 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.82 Å

EMDB-7985:
Cytoplasmic domain of class 2 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.94 Å

EMDB-7986, PDB-6dqz:
Class 4 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 6.01 Å

EMDB-7987, PDB-6dr0:
Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 4.47 Å

EMDB-7988, PDB-6dr2:
Ca2+-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 4.33 Å

EMDB-7989:
Cytoplasmic domain of Ca2+-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 4.69 Å

EMDB-7990:
Transmembrane domain of Ca2+-bound human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 4.22 Å

EMDB-7991, PDB-6dra:
Low IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.96 Å

EMDB-7992:
Cytoplasmic domain of low IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-7993:
Transmembrane domain of low IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-7994, PDB-6drc:
High IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-7995:
Transmembrane domain of high IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-7996:
Cytoplasmic domain of high IP3 Ca2+ human type 3 1,4,5-inositol trisphosphate receptor
Method: EM (single particle) / Resolution: 3.78 Å

Chemicals

ChemComp-ZN:
Unknown entry

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

ChemComp-CA:
Unknown entry

Source
  • homo sapiens (human)
KeywordsMETAL TRANSPORT / Ion channel / Calcium channel

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