8UXM

Structure of PKA phosphorylated human RyR2-R420W in the open state in the presence of calcium and calmodulin

PDB DOI: https://doi.org/10.2210/pdb8UXM/pdb
EM Map EMD-42769: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): Yes

Deposited: 2023-11-09 Released: 2023-11-22
Deposition Author(s): Miotto, M.C., Marks, A.R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.56 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders

Miotto, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 2,380.99 kDa
Atom Count: 143,464
Modelled Residue Count: 17,924
Deposited Residue Count: 20,896
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	A [auth I], G [auth J], H [auth L], I [auth K]	149	Homo sapiens	Mutation(s): 0 Gene Names: CALM1, CALM, CAM, CAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23 Go to UniProtKB: P0DP23
PHAROS: P0DP23 GTEx: ENSG00000198668
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DP23
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 2	B [auth A], J [auth B], K [auth C], L [auth D]	4,967	Homo sapiens	Mutation(s): 1 Gene Names: RYR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92736 (Homo sapiens) Explore Q92736 Go to UniProtKB: Q92736
PHAROS: Q92736 GTEx: ENSG00000198626
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92736
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	C [auth E], D [auth F], E [auth G], F [auth H]	108	Homo sapiens	Mutation(s): 0 Gene Names: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens) Explore P68106 Go to UniProtKB: P68106
PHAROS: P68106 GTEx: ENSG00000119782
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68106
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain JA [auth B] SDF format, chain LA [auth C] SDF format, chain NA [auth C] SDF format, chain PA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain T [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth A]	HA [auth B] JA [auth B] LA [auth C] NA [auth C] PA [auth D] HA [auth B], JA [auth B], LA [auth C], NA [auth C], PA [auth D], R [auth A], RA [auth D], T [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain HA [auth B] Focus chain JA [auth B] Focus chain LA [auth C] Focus chain NA [auth C] Focus chain PA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain T [auth A] Interactions & Density Focus chain HA [auth B] Focus chain JA [auth B] Focus chain LA [auth C] Focus chain NA [auth C] Focus chain PA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain T [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain KA [auth C] SDF format, chain OA [auth D] SDF format, chain Q [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain Q [auth A]	GA [auth B], KA [auth C], OA [auth D], Q [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain KA [auth C] Focus chain OA [auth D] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth B] Focus chain KA [auth C] Focus chain OA [auth D] Focus chain Q [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth L] SDF format, chain CA [auth K] SDF format, chain DA [auth K] SDF format, chain EA [auth K] SDF format, chain FA [auth K] SDF format, chain IA [auth B] SDF format, chain M [auth I] SDF format, chain MA [auth C] SDF format, chain N [auth I] SDF format, chain O [auth I] SDF format, chain P [auth I] SDF format, chain QA [auth D] SDF format, chain S [auth A] SDF format, chain U [auth J] SDF format, chain V [auth J] SDF format, chain W [auth J] SDF format, chain X [auth J] SDF format, chain Y [auth L] SDF format, chain Z [auth L] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth K] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth K] MOL2 format, chain IA [auth B] MOL2 format, chain M [auth I] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth I] MOL2 format, chain O [auth I] MOL2 format, chain P [auth I] MOL2 format, chain QA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain U [auth J] MOL2 format, chain V [auth J] MOL2 format, chain W [auth J] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth L]	AA [auth L] BA [auth L] CA [auth K] DA [auth K] EA [auth K] AA [auth L], BA [auth L], CA [auth K], DA [auth K], EA [auth K], FA [auth K], IA [auth B], M [auth I], MA [auth C], N [auth I], O [auth I], P [auth I], QA [auth D], S [auth A], U [auth J], V [auth J], W [auth J], X [auth J], Y [auth L], Z [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth K] Focus chain IA [auth B] Focus chain M [auth I] Focus chain MA [auth C] Focus chain N [auth I] Focus chain O [auth I] Focus chain P [auth I] Focus chain QA [auth D] Focus chain S [auth A] Focus chain U [auth J] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth J] Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth K] Focus chain IA [auth B] Focus chain M [auth I] Focus chain MA [auth C] Focus chain N [auth I] Focus chain O [auth I] Focus chain P [auth I] Focus chain QA [auth D] Focus chain S [auth A] Focus chain U [auth J] Focus chain V [auth J] Focus chain W [auth J] Focus chain X [auth J] Focus chain Y [auth L] Focus chain Z [auth L]