6DR0

Class 5 IP3-bound human type 3 1,4,5-inositol trisphosphate receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the regulation of inositol trisphosphate receptors by Ca2+and IP3.

Paknejad, N.Hite, R.K.

(2018) Nat Struct Mol Biol 25: 660-668

  • DOI: https://doi.org/10.1038/s41594-018-0089-6
  • Primary Citation of Related Structures:  
    6DQJ, 6DQN, 6DQS, 6DQV, 6DQZ, 6DR0, 6DR2, 6DRA, 6DRC

  • PubMed Abstract: 

    Inositol trisphosphate receptors (IP 3 Rs) are ubiquitous Ca 2+ -permeable channels that mediate release of Ca 2+ from the endoplasmic reticulum, thereby regulating numerous processes including cell division, cell death, differentiation and fertilization. IP 3 Rs are jointly activated by inositol trisphosphate (IP 3 ) and their permeant ion, Ca 2+ . At high concentrations, however, Ca 2+ inhibits activity, ensuring precise spatiotemporal control over intracellular Ca 2+ . Despite extensive characterization of IP 3 R, the mechanisms through which these molecules control channel gating have remained elusive. Here, we present structures of full-length human type 3 IP 3 Rs in ligand-bound and ligand-free states. Multiple IP 3 -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 2+ reveal two Ca 2+ -binding sites that induce the disruption of numerous interactions between subunits, thereby inhibiting IP 3 R. These structures thus provide a mechanistic basis for beginning to understand the regulation of IP 3 R.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol 1,4,5-trisphosphate receptor type 3
A, B, C, D
2,671Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14573
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3P
Query on I3P

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I3P BindingDB:  6DR0 Kd: 195 (nM) from 1 assay(s)
IC50: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references