8VK4

Structure of mouse RyR1 in complex with S100A1 (high-Ca2+/CFF/ATP dataset)

PDB DOI: https://doi.org/10.2210/pdb8VK4/pdb
EM Map EMD-43304: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-08 Released: 2024-02-07
Deposition Author(s): Weninger, G., 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 insights into the regulation of RyR1 by S100A1.

Weninger, G.

To be published.

Macromolecule Content

Total Structure Weight: 2,406.86 kDa
Atom Count: 149,304
Modelled Residue Count: 18,688
Deposited Residue Count: 21,324
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A [auth E], D [auth F], E [auth G], F [auth H]	108	Mus musculus	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for P26883 (Mus musculus) Explore P26883 Go to UniProtKB: P26883
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26883
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100A1	B [auth I] C [auth J] K L M [auth N] B [auth I], C [auth J], K, L, M [auth N], N [auth M], O, P	94	Mus musculus	Mutation(s): 0 Gene Names: S100a1
UniProt & NIH Common Fund Data Resources
Find proteins for Q91V77 (Mus musculus) Explore Q91V77 Go to UniProtKB: Q91V77
IMPC: MGI:1338917
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91V77
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	G [auth D], H [auth A], I [auth B], J [auth C]	5,035	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for E9PZQ0 (Mus musculus) Explore E9PZQ0 Go to UniProtKB: E9PZQ0
IMPC: MGI:99659
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E9PZQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth C] SDF format, chain VA [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain Z [auth D]	AA [auth D] GA [auth A] HA [auth A] NA [auth B] OA [auth B] AA [auth D], GA [auth A], HA [auth A], NA [auth B], OA [auth B], PA [auth C], VA [auth C], Z [auth D]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain AA [auth D] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth C] Focus chain VA [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth C] Focus chain VA [auth C] Focus chain Z [auth D]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain FA [auth A] SDF format, chain KA [auth B] SDF format, chain MA [auth B] SDF format, chain SA [auth C] SDF format, chain UA [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth D]	DA [auth A] FA [auth A] KA [auth B] MA [auth B] SA [auth C] DA [auth A], FA [auth A], KA [auth B], MA [auth B], SA [auth C], UA [auth C], W [auth D], Y [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain DA [auth A] Focus chain FA [auth A] Focus chain KA [auth B] Focus chain MA [auth B] Focus chain SA [auth C] Focus chain UA [auth C] Focus chain W [auth D] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth A] Focus chain FA [auth A] Focus chain KA [auth B] Focus chain MA [auth B] Focus chain SA [auth C] Focus chain UA [auth C] Focus chain W [auth D] Focus chain Y [auth D]
CFF (Subject of Investigation/LOI) Query on CFF Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain JA [auth B] SDF format, chain RA [auth C] SDF format, chain V [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain V [auth D]	CA [auth A], JA [auth B], RA [auth C], V [auth D]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain JA [auth B] Focus chain RA [auth C] Focus chain V [auth D] Interactions & Density Focus chain CA [auth A] Focus chain JA [auth B] Focus chain RA [auth C] Focus chain V [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain IA [auth B] SDF format, chain QA [auth C] SDF format, chain U [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain U [auth D]	BA [auth A], IA [auth B], QA [auth C], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain IA [auth B] Focus chain QA [auth C] Focus chain U [auth D] Interactions & Density Focus chain BA [auth A] Focus chain IA [auth B] Focus chain QA [auth C] Focus chain U [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AB [auth N] SDF format, chain BB [auth N] SDF format, chain CB [auth M] SDF format, chain DB [auth M] SDF format, chain EA [auth A] SDF format, chain EB [auth O] SDF format, chain FB [auth O] SDF format, chain GB [auth P] SDF format, chain HB [auth P] SDF format, chain LA [auth B] SDF format, chain Q [auth I] SDF format, chain R [auth I] SDF format, chain S [auth J] SDF format, chain T [auth J] SDF format, chain TA [auth C] SDF format, chain WA [auth K] SDF format, chain X [auth D] SDF format, chain XA [auth K] SDF format, chain YA [auth L] SDF format, chain ZA [auth L] MOL2 format, chain AB [auth N] MOL2 format, chain BB [auth N] MOL2 format, chain CB [auth M] MOL2 format, chain DB [auth M] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth O] MOL2 format, chain FB [auth O] MOL2 format, chain GB [auth P] MOL2 format, chain HB [auth P] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth I] MOL2 format, chain R [auth I] MOL2 format, chain S [auth J] MOL2 format, chain T [auth J] MOL2 format, chain TA [auth C] MOL2 format, chain WA [auth K] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth K] MOL2 format, chain YA [auth L] MOL2 format, chain ZA [auth L]	AB [auth N] BB [auth N] CB [auth M] DB [auth M] EA [auth A] AB [auth N], BB [auth N], CB [auth M], DB [auth M], EA [auth A], EB [auth O], FB [auth O], GB [auth P], HB [auth P], LA [auth B], Q [auth I], R [auth I], S [auth J], T [auth J], TA [auth C], WA [auth K], X [auth D], XA [auth K], YA [auth L], ZA [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth M] Focus chain DB [auth M] Focus chain EA [auth A] Focus chain EB [auth O] Focus chain FB [auth O] Focus chain GB [auth P] Focus chain HB [auth P] Focus chain LA [auth B] Focus chain Q [auth I] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth J] Focus chain TA [auth C] Focus chain WA [auth K] Focus chain X [auth D] Focus chain XA [auth K] Focus chain YA [auth L] Focus chain ZA [auth L] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth M] Focus chain DB [auth M] Focus chain EA [auth A] Focus chain EB [auth O] Focus chain FB [auth O] Focus chain GB [auth P] Focus chain HB [auth P] Focus chain LA [auth B] Focus chain Q [auth I] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth J] Focus chain TA [auth C] Focus chain WA [auth K] Focus chain X [auth D] Focus chain XA [auth K] Focus chain YA [auth L] Focus chain ZA [auth L]