7LHE | pdb_00007lhe

Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state

PDB DOI: https://doi.org/10.2210/pdb7LHE/pdb
EM Map EMD-23337: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2021-01-22 Released: 2021-06-02
Deposition Author(s): Baker, M.R., Fan, G., Baker, M.L., Serysheva, I.I.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Welch Foundation, American Heart Association, National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of type 1 IP3R channel in a lipid bilayer

Baker, M.R., Fan, G., Seryshev, A.B., Agosto, M.A., Baker, M.L., Serysheva, I.I.

(2021) Commun Biol 4: 625

DOI: https://doi.org/10.1038/s42003-021-02156-4

Macromolecule Content

Total Structure Weight: 1,269.13 kDa
Atom Count: 73,691
Modeled Residue Count: 9,192
Deposited Residue Count: 10,936
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 1,4,5-trisphosphate receptor type 1	A, B [auth D], C, D [auth B]	2,734	Rattus norvegicus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P29994 (Rattus norvegicus) Explore P29994 Go to UniProtKB: P29994
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29994
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLX (Subject of Investigation/LOI) Query on PLX Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain S [auth D] SDF format, chain X [auth C] SDF format, chain Z [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain R [auth D] SDF format, chain IA [auth B] SDF format, chain CA [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain S [auth D] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain S [auth D] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain CA [auth B]	AA [auth C] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth C], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth D], N [auth D], O [auth D], P [auth D], R [auth D], S [auth D], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth C]	(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 C₄₂ H₈₉ N O₈ P YVNJQRQLQPWVSQ-IWSHAHEXSA-O		Interactions Focus chain AA [auth C] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain Q [auth D] SDF format, chain Y [auth C] SDF format, chain I [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain I [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain I [auth A]	I [auth A], JA [auth B], Q [auth D], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain JA [auth B] Focus chain Q [auth D] Focus chain Y [auth C] Interactions & Density Focus chain I [auth A] Focus chain JA [auth B] Focus chain Q [auth D] Focus chain Y [auth C]

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
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM072804
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R21NS106968
Welch Foundation	United States	AU-2014-20190330
American Heart Association	United States	18CDA34110086
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01GM063210
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01EY025218
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	R01EY026545