9kp6

Cryo-EM structure of mouse bestrophin-1 in a closed state

Method: ELECTRON MICROSCOPY Dmax: 119.4 Å Quality: GOOD

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

Bestrophin-1,Soluble cytochrome b562

Mus musculus

UniProt O88870

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–551 Chain B; UniProt 1–551 Chain C; UniProt 1–551 Chain D; UniProt 1–551 Chain E; UniProt 1–551 Not recorded CA CALCIUM ION × 5 CL CHLORIDE ION × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.18 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BEST1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–551; UniProt 1–551 Author chain B; PDBConstruct 1–551; UniProt 1–551 Author chain C; PDBConstruct 1–551; UniProt 1–551 Author chain D; PDBConstruct 1–551; UniProt 1–551 Author chain E; PDBConstruct 1–551; UniProt 1–551

Bestrophin-1,Soluble cytochrome b562

Mus musculus

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 23–128 Chain B; UniProt 23–128 Chain C; UniProt 23–128 Chain D; UniProt 23–128 Chain E; UniProt 23–128 Not recorded CA CALCIUM ION × 5 CL CHLORIDE ION × 10 ELECTRON MICROSCOPY cryo-EM buffer:pH 8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.18 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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 562–667; UniProt 23–128 Author chain B; PDBConstruct 562–667; UniProt 23–128 Author chain C; PDBConstruct 562–667; UniProt 23–128 Author chain D; PDBConstruct 562–667; UniProt 23–128 Author chain E; PDBConstruct 562–667; UniProt 23–128

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 9kp6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9kp6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9kp6
Deposition date deposition_date2024-11-22
Structure title titleCryo-EM structure of mouse bestrophin-1 in a closed state
Keywords keywordsClosed, Calcium-bound, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier37.93
Radius of gyration Rg (electron density) rg_electron36.83
Forward intensity I(0) i0598639000.00
Molecular weight molecular_weight212530.0 kDa
Excluded volume excluded_volume270820 ų
Envelope volume envelope_volume347780 ų
Hydration-shell volume shell_volume74091 ų
Envelope diameter envelope_diameter118.3
Shell Rg shell_rg46.20
Envelope Rg envelope_rg36.78
Shape Rg shape_rg36.79
Total Rg total_rg37.54
Total atoms total_atoms15005
Residues n_residues1825
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 dmax119.4
Rg (real space) rg_real37.71
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real5.9860e+08
I(0) uncertainty (real space) i0_real_error1.0350e+07
Rg (reciprocal space) rg_reciprocal37.85
I(0) (reciprocal space) i0_reciprocal598700000.0000
Solution quality estimate total_estimate0.8155
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.3
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.385
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha200800000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)