8rru

Structure of RyR1 reconstituted into lipid liposomes in primed state in complex with FKBP and Nb9657.

Method: ELECTRON MICROSCOPY Dmax: 326.7 Å Quality: EXCELLENT

1. Protein Identity and Related Structures Protein Identity & Related Structures

Peptidyl-prolyl cis-trans isomerase FKBP1B

OrganismNot specified

UniProt Q8HYX6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric(12) Consistent with protein copy count Chain A; UniProt 2–108 Chain D; UniProt 2–108 Chain H; UniProt 2–108 Chain I; UniProt 2–108 Not recorded Ryanodine receptor 1 × 4 (P11716) Nanobody 9657 × 4 ZN ZINC ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 CFF CAFFEINE × 4 CA CALCIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FKB1B_RABIT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–107; UniProt 2–108 Author chain D; PDBConstruct 1–107; UniProt 2–108 Author chain H; PDBConstruct 1–107; UniProt 2–108 Author chain I; PDBConstruct 1–107; UniProt 2–108

Ryanodine receptor 1

OrganismNot specified

UniProt P11716

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 12 PDB declaration: 12-meric(12) Consistent with protein copy count Chain B; UniProt 11–5037 Chain E; UniProt 11–5037 Chain G; UniProt 11–5037 Chain J; UniProt 11–5037 Not recorded Peptidyl-prolyl cis-trans isomerase FKBP1B × 4 (Q8HYX6) Nanobody 9657 × 4 ZN ZINC ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 CFF CAFFEINE × 4 CA CALCIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

124 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RYR1_RABIT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–5027; UniProt 11–5037 Author chain E; PDBConstruct 1–5027; UniProt 11–5037 Author chain G; PDBConstruct 1–5027; UniProt 11–5037 Author chain J; PDBConstruct 1–5027; UniProt 11–5037

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8rru

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8rru
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8rru
Deposition date deposition_date2024-01-23
Structure title titleStructure of RyR1 reconstituted into lipid liposomes in primed state in complex with FKBP and Nb9657.
Keywords keywordsIon channel, Ca2+, tetramer, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier
Radius of gyration Rg (electron density) rg_electron110.00
Forward intensity I(0) i056936500000.00
Molecular weight molecular_weight2046100.0 kDa
Excluded volume excluded_volume2561000 ų
Envelope volume envelope_volume5012900 ų
Hydration-shell volume shell_volume380130 ų
Envelope diameter envelope_diameter389.7
Shell Rg shell_rg106.40
Envelope Rg envelope_rg105.40
Shape Rg shape_rg110.10
Total Rg total_rg109.90
Total atoms total_atoms143883
Residues n_residues18208
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax326.7
Rg (real space) rg_real109.90
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real5.5170e+10
I(0) uncertainty (real space) i0_real_error1.0960e+09
Rg (reciprocal space) rg_reciprocal109.90
I(0) (reciprocal space) i0_reciprocal56810000000.0000
Solution quality estimate total_estimate0.9016
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary140.0
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.0700 −1
Current regularization parameter α current_alpha1.9620
Highest regularization parameter α highest_alpha7239000000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.993; Stabil: 0.920; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)