8epm

Human R-type voltage-gated calcium channel Cav2.3 CH2II-deleted mutant at 3.1 Angstrom resolution

Method: ELECTRON MICROSCOPY Dmax: 151.5 Å Quality: GOOD

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

Voltage-dependent R-type calcium channel subunit alpha-1E

Homo sapiens

UniProt Q15878

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 5 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–2313 Not recorded Voltage-dependent calcium channel subunit alpha-2/delta-1 × 1 (P54289) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAC1E_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–2313; UniProt 1–2313

Voltage-dependent calcium channel subunit alpha-2/delta-1

Homo sapiens

UniProt P54289

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 5 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–1103 Not recorded Voltage-dependent R-type calcium channel subunit alpha-1E × 1 (Q15878) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.10 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.

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CA2D1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1103; UniProt 1–1103

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 8epm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8epm
Deposition date deposition_date2022-10-06
Structure title titleHuman R-type voltage-gated calcium channel Cav2.3 CH2II-deleted mutant at 3.1 Angstrom resolution
Keywords keywordsCav2.3, Channels, Calcium Ion-Selective, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier47.01
Radius of gyration Rg (electron density) rg_electron47.50
Forward intensity I(0) i0648407000.00
Molecular weight molecular_weight219330.0 kDa
Excluded volume excluded_volume277800 ų
Envelope volume envelope_volume404750 ų
Hydration-shell volume shell_volume71532 ų
Envelope diameter envelope_diameter156.1
Shell Rg shell_rg51.09
Envelope Rg envelope_rg46.53
Shape Rg shape_rg47.48
Total Rg total_rg47.71
Total atoms total_atoms15458
Residues n_residues1939
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 dmax151.5
Rg (real space) rg_real47.08
Rg uncertainty (real space) rg_real_error1.59
I(0) (real space) i0_real6.4840e+08
I(0) uncertainty (real space) i0_real_error1.2440e+07
Rg (reciprocal space) rg_reciprocal47.01
I(0) (reciprocal space) i0_reciprocal648300000.0000
Solution quality estimate total_estimate0.8653
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.0
Skewness Skewness skewness0.322
Kurtosis Kurtosis kurtosis-0.541
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha62760000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.441

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)