SAXSdb — 2be6

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

Calmodulin 2

Homo sapiens

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 1–149	Not recorded	Voltage-dependent L-type calcium channel alpha-1C subunit × 1 （Q13933） CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–149	Not recorded	Voltage-dependent L-type calcium channel alpha-1C subunit × 1 （Q13933） CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–149	Not recorded	Voltage-dependent L-type calcium channel alpha-1C subunit × 1 （Q13933） CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–149 Chain C； UniProt 1–149	Not recorded	Voltage-dependent L-type calcium channel alpha-1C subunit × 2 （Q13933） CA CALCIUM ION × 8 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q53S29_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain B； PDBConstruct 1–149； UniProt 1–149 Author chain C； PDBConstruct 1–149； UniProt 1–149

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

Homo sapiens

UniProt Q13933

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 D； UniProt 1659–1692	Fragment：IQ domain, residues 1659-1692	Calmodulin 2 × 1 （Q53S29） CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1659–1692	Fragment：IQ domain, residues 1659-1692	Calmodulin 2 × 1 （Q53S29） CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1659–1692	Fragment：IQ domain, residues 1659-1692	Calmodulin 2 × 1 （Q53S29） CA CALCIUM ION × 4 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1659–1692 Chain F； UniProt 1659–1692	Fragment：IQ domain, residues 1659-1692	Calmodulin 2 × 2 （Q53S29） CA CALCIUM ION × 8 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；284 K；0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.255

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.

Other PDB	Difference from Current Entry 2BE6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2F3Y Calmodulin/IQ domain complex Deposited 2005-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1665–1685（21 aa）	Not recorded	CA CALCIUM ION × 4 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；32% PEG 4000, 50mM TRIS, 50 mM MgCl2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.45 Å R-free 0.219
2F3Z Calmodulin/IQ-AA domain complex Deposited 2005-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1665–1685（21 aa）	Mutation：I1672A, Q1673A	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；298 K；32% PEG 4000, 50mM TRIS, 50 mM MgCl2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.272

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

View Construct and Data Evidence

UniProt name	CAC1C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 4–37； UniProt 1659–1692 Author chain E； PDBConstruct 4–37； UniProt 1659–1692 Author chain F； PDBConstruct 4–37； UniProt 1659–1692

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2be6
Deposition date deposition_date	2005-10-23
Structure title title	2.0 A crystal structure of the CaV1.2 IQ domain-Ca/CaM complex
Keywords keywords	calmodulin, calcium channel, IQ domain, inactivation, facilitation, calcium-dependent, gating, voltage-gated, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.80 Å
Radius of gyration Rg (electron density) rg_electron	26.81 Å
Forward intensity I(0) i0	51973500.00
Molecular weight molecular_weight	54309.0 kDa
Excluded volume excluded_volume	67070 Å³
Envelope volume envelope_volume	85764 Å³
Hydration-shell volume shell_volume	27415 Å³
Envelope diameter envelope_diameter	88.3 Å
Shell Rg shell_rg	33.22 Å
Envelope Rg envelope_rg	26.46 Å
Shape Rg shape_rg	26.82 Å
Total Rg total_rg	27.50 Å
Total atoms total_atoms	3780
Residues n_residues	483
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.2 Å
Rg (real space) rg_real	27.68 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	5.1970e+07
I(0) uncertainty (real space) i0_real_error	7.0400e+05
Rg (reciprocal space) rg_reciprocal	27.72 Å
I(0) (reciprocal space) i0_reciprocal	51970000.0000
Solution quality estimate total_estimate	0.9137
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.8 Å
Skewness Skewness skewness	0.128
Kurtosis Kurtosis kurtosis	-0.595
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7051000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Calmodulin 2
Molecular weight formula_weight	16965.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4120

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAKL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Voltage-dependent L-type calcium channel alpha-1C subunit
Molecular weight formula_weight	4373.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

GHMDEVTVGKFYATFLIQEYFRKFKKRKEQGLVGKPS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2be6a_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

Domain ID domain_id	d2be6b_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

Domain ID domain_id	d2be6c_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

CATH v4.4 (6 domains)

Domain ID domain_id	2be6A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2be6A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2be6B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2be6B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2be6C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2be6C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	84.731 Å
Unit-cell length b length_b	37.241 Å
Unit-cell length c length_c	86.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2050
R_work r_work	0.2020
R_free r_free	0.2550

fit	/app/data/saxs_computation/be/2be6/2be6.fit
pddf	/app/data/pr_computation/be/2be6/2be6.pr.out
profile	/app/data/saxs_computation/be/2be6/2be6.dat

2.0 A crystal structure of the CaV1.2 IQ domain-Ca/CaM complex

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

Calmodulin 2

State in the Current Structure

Other States of the Same Protein in the Database

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

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)