1t0j

Crystal structure of a complex between voltage-gated calcium channel beta2a subunit and a peptide of the alpha1c subunit

Method: X-RAY DIFFRACTION Dmax: 79.0 Å Quality: REASONABLE

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

voltage-gated calcium channel subunit beta2a

Rattus norvegicus

UniProt Q8VGC3

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 17–145 Chain B; UniProt 203–425 Fragment:residues 17-145 Fragment:residues 203-425 Voltage-dependent L-type calcium channel alpha-1C subunit × 1 (Q13936) CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;Tris-Cl, PEG 4000, NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 17–145 Chain B; UniProt 203–425 Fragment:residues 17-145 Fragment:residues 203-425 Voltage-dependent L-type calcium channel alpha-1C subunit × 1 (Q13936) CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;Tris-Cl, PEG 4000, NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.242

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CACB2_RAT
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 4–132; UniProt 17–145 Author chain B; PDBConstruct 3–224; UniProt 203–425

Voltage-dependent L-type calcium channel alpha-1C subunit

Homo sapiens

UniProt Q13936

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 428–445 Fragment:Residues 428-443 voltage-gated calcium channel subunit beta2a × 1 (Q8VGC3) voltage-gated calcium channel subunit beta2a × 1 (Q8VGC3) CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;Tris-Cl, PEG 4000, NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 428–445 Fragment:Residues 428-443 voltage-gated calcium channel subunit beta2a × 1 (Q8VGC3) voltage-gated calcium channel subunit beta2a × 1 (Q8VGC3) CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;Tris-Cl, PEG 4000, NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.242

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.

23 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAC1C_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 3–20; UniProt 428–445

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 1t0j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t0j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t0j
Deposition date deposition_date2004-04-09
Structure title titleCrystal structure of a complex between voltage-gated calcium channel beta2a subunit and a peptide of the alpha1c subunit
Keywords keywordsSH3 domain, nucleotide kinase like domain, ion channel, calcium channel, AID, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.61
Radius of gyration Rg (electron density) rg_electron22.52
Forward intensity I(0) i019365300.00
Molecular weight molecular_weight33632.0 kDa
Excluded volume excluded_volume42282 ų
Envelope volume envelope_volume52592 ų
Hydration-shell volume shell_volume20394 ų
Envelope diameter envelope_diameter82.6
Shell Rg shell_rg28.42
Envelope Rg envelope_rg23.04
Shape Rg shape_rg22.49
Total Rg total_rg23.43
Total atoms total_atoms2368
Residues n_residues299
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 dmax79.0
Rg (real space) rg_real23.70
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real1.9370e+07
I(0) uncertainty (real space) i0_real_error2.6330e+05
Rg (reciprocal space) rg_reciprocal23.68
I(0) (reciprocal space) i0_reciprocal19370000.0000
Solution quality estimate total_estimate0.6263
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.2
Skewness Skewness skewness0.432
Kurtosis Kurtosis kurtosis-0.323
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4809000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.801; Stabil: 0.991; Sysdev: 0.286; Positv: 1.000; Valcen: 0.904; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1t0ja_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.2 — SH3-domain
Family Family familyb.34.2.1 — SH3-domain
Domain ID domain_idd1t0jb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.1 — Nucleotide and nucleoside kinases
Domain ID domain_idd1t0jc_
Class classj — Peptides
Fold Fold foldj.68 — Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor)
Superfamily Superfamily superfamilyj.68.1 — Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor)
Family Family familyj.68.1.1 — Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor)

CATH v4.4 (2 domains)

Domain ID domain_id1t0jA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily40 — SH3 Domains
Domain ID domain_id1t0jB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)