3bya

Structure of a Calmodulin Complex

Method: X-RAY DIFFRACTION Dmax: 50.9 Å Quality: EXCELLENT

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 Glutamate [NMDA] receptor subunit zeta-1 peptide × 1 (Q05586) CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;17-19% PEG 3350, 0.120mM Ammonium Phosphate, 15% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.85 Å R-free 0.232

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

Glutamate [NMDA] receptor subunit zeta-1 peptide

OrganismNot specified

UniProt Q05586

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 875–898 Not recorded Calmodulin × 1 (P62158) CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;17-19% PEG 3350, 0.120mM Ammonium Phosphate, 15% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.85 Å R-free 0.232

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.

83 other PDB entries and 86 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NMDZ1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–24; UniProt 875–898

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 3bya

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3bya
Deposition date deposition_date2008-01-15
Structure title titleStructure of a Calmodulin Complex
Keywords keywords;Calmodulin, EF hand motif, NR1, N-methyl-D-aspartate receptor, glutamate, central nervous system, neuronal channel, calcium channel, Methylation, Phosphoprotein, Cell junction, Glycoprotein, Ion transport, Ionic channel, Magnesium, Membrane, Postsynaptic cell membrane, Synapse, Transmembrane, Transport, METAL BINDING PROTEIN ;; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.66
Radius of gyration Rg (electron density) rg_electron15.19
Forward intensity I(0) i06603230.00
Molecular weight molecular_weight17852.0 kDa
Excluded volume excluded_volume21977 ų
Envelope volume envelope_volume25049 ų
Hydration-shell volume shell_volume13977 ų
Envelope diameter envelope_diameter49.4
Shell Rg shell_rg20.94
Envelope Rg envelope_rg15.38
Shape Rg shape_rg15.20
Total Rg total_rg16.18
Total atoms total_atoms1243
Residues n_residues157
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 dmax50.9
Rg (real space) rg_real16.56
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real6.6030e+06
I(0) uncertainty (real space) i0_real_error7.2270e+04
Rg (reciprocal space) rg_reciprocal16.57
I(0) (reciprocal space) i0_reciprocal6603000.0000
Solution quality estimate total_estimate0.9048
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.1
Skewness Skewness skewness0.111
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.4800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha873500.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.985

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_idd3byaa_
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_id3byaA00
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)