8UXL

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

PDB DOI: https://doi.org/10.2210/pdb8UXL/pdb
EM Map EMD-42768: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
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: 3.12 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: 143,500
Modelled Residue Count: 17,928
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
Ryanodine receptor 2	A, G [auth B], H [auth C], I [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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	B [auth E], C [auth F], D [auth G], E [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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	F [auth I], J, K [auth L], L [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

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