7T3Q | pdb_00007t3q

IP3 and ATP bound type 3 IP3 receptor in the pre-active B state

PDB DOI: https://doi.org/10.2210/pdb7T3Q/pdb
EM Map EMD-25668: EMDB EMDataResource

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM mpstruc

Deposited: 2021-12-08 Released: 2022-03-23
Deposition Author(s): Schmitz, E.A., Takahashi, H., Karakas, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for activation and gating of IP 3 receptors.

Schmitz, E.A., Takahashi, H., Karakas, E.

(2022) Nat Commun 13: 1408-1408

PubMed: 35301323 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-29073-2
Primary Citation Related Structures:
7T3P, 7T3Q, 7T3R, 7T3T, 7T3U

PubMed Abstract:
A pivotal component of the calcium (Ca ²⁺) signaling toolbox in cells is the inositol 1,4,5-triphosphate (IP ₃) receptor (IP ₃R), which mediates Ca ²⁺ release from the endoplasmic reticulum (ER), controlling cytoplasmic and organellar Ca ²⁺ concentrations. IP ₃Rs are co-activated by IP ₃ and Ca ²⁺, inhibited by Ca ²⁺ at high concentrations, and potentiated by ATP. However, the underlying molecular mechanisms are unclear. Here we report cryo-electron microscopy (cryo-EM) structures of human type-3 IP ₃R obtained from a single dataset in multiple gating conformations: IP ₃-ATP bound pre-active states with closed channels, IP ₃-ATP-Ca ²⁺ bound active state with an open channel, and IP ₃-ATP-Ca ²⁺ bound inactive state with a closed channel. The structures demonstrate how IP ₃-induced conformational changes prime the receptor for activation by Ca ²⁺, how Ca ²⁺ binding leads to channel opening, and how ATP modulates the activity, providing insights into the long-sought questions regarding the molecular mechanism underpinning receptor activation and gating.

Organizational Affiliation

Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA.

Macromolecule Content

Total Structure Weight: 1,201.27 kDa
Atom Count: 68,124
Modeled Residue Count: 8,412
Deposited Residue Count: 10,532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 1,4,5-trisphosphate receptor type 3	A, B, C, D	2,633	Homo sapiens	Mutation(s): 0 Gene Names: ITPR3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q14573 (Homo sapiens) Explore Q14573 Go to UniProtKB: Q14573
PHAROS: Q14573 GTEx: ENSG00000096433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14573
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B]	G [auth A], J [auth B], M [auth C], P [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
I3P Query on I3P Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C₆ H₁₅ O₁₅ P₃ MMWCIQZXVOZEGG-XJTPDSDZSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
I3P	BindingDB: 7T3Q	Kd: 195 (nM) from 1 assay(s)
I3P	BindingDB: 7T3Q	IC50: 1.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Schmitz, E.A.

Takahashi, H.

Karakas, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM141251
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30DK020593
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008320

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2022-05-04
Changes: Database references
Version 1.2: 2024-10-30
Changes: Data collection, Refinement description, Structure summary