7miy

Human N-type voltage-gated calcium channel Cav2.2 at 3.1 Angstrom resolution

Method: ELECTRON MICROSCOPY Dmax: 207.4 Å Quality: GOOD

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

Voltage-dependent N-type calcium channel subunit alpha-1B

Homo sapiens

UniProt Q00975

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 × 3 其他Polymer 5 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–2339 Not recorded Voltage-dependent L-type calcium channel subunit beta-3 × 1 (P54284) 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;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 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 3 CLR CHOLESTEROL × 4 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot for 6 seconds before plunging 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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAC1B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–2339; UniProt 1–2339

Voltage-dependent L-type calcium channel subunit beta-3

Homo sapiens

UniProt P54284

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 × 3 其他Polymer 5 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–484 Not recorded Voltage-dependent N-type calcium channel subunit alpha-1B × 1 (Q00975) 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;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 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 3 CLR CHOLESTEROL × 4 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot for 6 seconds before plunging 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.

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CACB3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–484; UniProt 1–484

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 × 3 其他Polymer 5 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–1103 Not recorded Voltage-dependent N-type calcium channel subunit alpha-1B × 1 (Q00975) Voltage-dependent L-type calcium channel subunit beta-3 × 1 (P54284) ;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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;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 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 3 CLR CHOLESTEROL × 4 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;blot for 6 seconds before plunging 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 3
Chains and sequence ranges Author chain D; 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 7miy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7miy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7miy
Deposition date deposition_date2021-04-18
Structure title titleHuman N-type voltage-gated calcium channel Cav2.2 at 3.1 Angstrom resolution
Keywords keywordsCav2.2, 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_guinier59.66
Radius of gyration Rg (electron density) rg_electron59.53
Forward intensity I(0) i01210970000.00
Molecular weight molecular_weight304980.0 kDa
Excluded volume excluded_volume387630 ų
Envelope volume envelope_volume603020 ų
Hydration-shell volume shell_volume90077 ų
Envelope diameter envelope_diameter230.0
Shell Rg shell_rg54.41
Envelope Rg envelope_rg60.56
Shape Rg shape_rg59.51
Total Rg total_rg59.41
Total atoms total_atoms21475
Residues n_residues2598
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 dmax207.4
Rg (real space) rg_real60.41
Rg uncertainty (real space) rg_real_error2.35
I(0) (real space) i0_real1.2110e+09
I(0) uncertainty (real space) i0_real_error2.7680e+07
Rg (reciprocal space) rg_reciprocal59.02
I(0) (reciprocal space) i0_reciprocal1208000000.0000
Solution quality estimate total_estimate0.8359
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.8
Skewness Skewness skewness0.674
Kurtosis Kurtosis kurtosis0.143
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha70560000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.559

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

8. Citations (1)

9. Files and Curves (10)