3dvk

Crystal Structure of Ca2+/CaM-CaV2.3 IQ domain complex

Method: X-RAY DIFFRACTION Dmax: 55.0 Å Quality: GOOD

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

Calmodulin

Homo sapiens

UniProt P62158

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–149 Not recorded Voltage-dependent R-type calcium channel subunit alpha-1E × 1 (Q07652) CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;292 K;0.1 M Bis-Tris, 25-30 % PEG 2000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.30 Å R-free 0.291

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.

105 other PDB entries and 176 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CALM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–148; UniProt 2–149

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

Rattus norvegicus

UniProt Q07652

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1818–1837 Fragment:UNP residues 1818-1837 Calmodulin × 1 (P62158) CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;292 K;0.1 M Bis-Tris, 25-30 % PEG 2000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K Resolution 2.30 Å R-free 0.291

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.

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

View Construct and Data Evidence
UniProt name CAC1E_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–23; UniProt 1818–1837

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 3dvk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dvk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dvk
Deposition date deposition_date2008-07-18
Structure title titleCrystal Structure of Ca2+/CaM-CaV2.3 IQ domain complex
Keywords keywordscalmodulin, calcium channel, IQ domain, inactivation, facilitation, calcium-dependent, voltage-gated, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.32
Radius of gyration Rg (electron density) rg_electron16.07
Forward intensity I(0) i06824890.00
Molecular weight molecular_weight17961.0 kDa
Excluded volume excluded_volume21924 ų
Envelope volume envelope_volume25921 ų
Hydration-shell volume shell_volume13974 ų
Envelope diameter envelope_diameter53.6
Shell Rg shell_rg21.27
Envelope Rg envelope_rg16.09
Shape Rg shape_rg16.10
Total Rg total_rg16.87
Total atoms total_atoms1249
Residues n_residues166
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 dmax55.0
Rg (real space) rg_real17.25
Rg uncertainty (real space) rg_real_error0.27
I(0) (real space) i0_real6.8250e+06
I(0) uncertainty (real space) i0_real_error7.8840e+04
Rg (reciprocal space) rg_reciprocal17.26
I(0) (reciprocal space) i0_reciprocal6825000.0000
Solution quality estimate total_estimate0.9000
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3
Skewness Skewness skewness0.221
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.4600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha880900.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3dvka_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like

CATH v4.4 (1 domains)

Domain ID domain_id3dvkA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (1)

9. Files and Curves (10)