SAXSdb — 2m5e

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

Calmodulin

Paramecium tetraurelia

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 77–149	Fragment：UNP residues 77-149	Sodium channel protein type 2 subunit alpha × 1 （P04775） CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Pressure ambient NMR sample composition：1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 100% D2O \| 100% D2O	Resolution not provided

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 2M5E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CLM STRUCTURE OF PARAMECIUM TETRAURELIA CALMODULIN AT 1.8 ANGSTROMS RESOLUTION Deposited 1993-01-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1EXR THE 1.0 ANGSTROM CRYSTAL STRUCTURE OF CA+2 BOUND CALMODULIN Deposited 2000-05-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；278 K；MPD, calcium chloride, sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 1.00 Å R-free 0.163
1N0Y Crystal Structure of Pb-bound Calmodulin Deposited 2002-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	PB LEAD (II) ION × 7 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；MPD, sodium cacodylate, sodium acetate, lead nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.223
1N0Y Crystal Structure of Pb-bound Calmodulin Deposited 2002-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–148（148 aa）	Not recorded	PB LEAD (II) ION × 7 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；MPD, sodium cacodylate, sodium acetate, lead nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.223
1OSA CRYSTAL STRUCTURE OF RECOMBINANT PARAMECIUM TETRAURELIA CALMODULIN AT 1.68 ANGSTROMS RESOLUTION Deposited 1993-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.68 Å
2KXW Structure of the C-domain Fragment of apo Calmodulin Bound to the IQ motif of Nav1.2 Deposited 2010-05-13	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 77–149（73 aa） Fragment：C-domain (UNP Residues 77-149)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 1.5 mM Voltage-dependent Sodium Channel v 1.2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM Voltage-dependent Sodium Channel v 1.2, 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 100% D2O \| 100% D2O	Resolution not provided
5E1K Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia SAD data Deposited 2015-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–149（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；50 mM sodium cacodylate, 50% MPD	Resolution 1.00 Å R-free 0.165
5E1N Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia qFit disorder model Deposited 2015-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–149（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；50 mM sodium cacodylate, 50% MPD	Resolution 1.00 Å R-free 0.150
5E1P Ca(2+)-Calmodulin from Paramecium tetraurelia qFit disorder model Deposited 2015-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；50 mM sodium cacodylate, 50% MPD	Resolution 1.01 Å R-free 0.142

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM_PARTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–73； UniProt 77–149

Sodium channel protein type 2 subunit alpha

Rattus norvegicus

UniProt P04775

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 1901–1927	Fragment：UNP residues 1901-1927	Calmodulin × 1 （P07463） CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Pressure ambient NMR sample composition：1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.5 mM [U-100% 13C; U-100% 15N] C-domain of Calmodulin, 1.5 mM IQ motif peptide of NaV1.2, 3.3 mM CALCIUM ION, 10 mM [U-2H] imidazole, 100 mM potassium chloride, 0.01 % sodium azide, 50 uM [U-2H] EDTA, 100% D2O \| 100% D2O	Resolution not provided

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 2M5E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BYY SODIUM CHANNEL IIA INACTIVATION GATE Deposited 1998-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1474–1526（53 aa） Fragment：INACTIVATION DOMAIN FRAGMENT	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；299 K NMR sample composition H2O/D2O	Resolution not provided
2KXW Structure of the C-domain Fragment of apo Calmodulin Bound to the IQ motif of Nav1.2 Deposited 2010-05-13	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1901–1927（27 aa） Fragment：IQ-motif of the Voltage-dependent Sodium Channel (UNP Residues 1901-1927)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 1.5 mM Voltage-dependent Sodium Channel v 1.2, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM Voltage-dependent Sodium Channel v 1.2, 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 100% D2O \| 100% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	SCN2A_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–27； UniProt 1901–1927

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	2m5e
Deposition date deposition_date	2013-02-21
Structure title title	Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2
Keywords keywords	;Calcium Binding Protein, NaV1.2, Ion Channel Gating, IQ Motif, Metal Binding, Sodium Channels, Metal Transport, Voltage Dependent, Voltage Gated, Calcium Binding Protein-Metal Transport Complex, Neuronal Peptides, EF-Hand, CALCIUM-BINDING PROTEIN-METAL TRANSPORT complex ;; CALCIUM-BINDING PROTEIN/METAL TRANSPORT
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.78 Å
Radius of gyration Rg (electron density) rg_electron	13.66 Å
Forward intensity I(0) i0	891873000.00
Molecular weight molecular_weight	247290.0 kDa
Excluded volume excluded_volume	307470 Å³
Envelope volume envelope_volume	32922 Å³
Hydration-shell volume shell_volume	16431 Å³
Envelope diameter envelope_diameter	60.8 Å
Shell Rg shell_rg	23.03 Å
Envelope Rg envelope_rg	17.57 Å
Shape Rg shape_rg	13.61 Å
Total Rg total_rg	14.00 Å
Total atoms total_atoms	34503
Residues n_residues	2100
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	50.3 Å
Rg (real space) rg_real	13.70 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	8.9190e+08
I(0) uncertainty (real space) i0_real_error	1.0520e+07
Rg (reciprocal space) rg_reciprocal	13.71 Å
I(0) (reciprocal space) i0_reciprocal	891900000.0000
Solution quality estimate total_estimate	0.7205
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.032
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	325900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.465; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Calmodulin
Molecular weight formula_weight	8416.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	34503

MKEQDSEEELIEAFKVFDRDGNGLISAAELRHVMTNLGEKLTDDEVDEMIREADIDGDGHINYEEFVRMMVSK

来源 Source

来源生物 organism	Paramecium tetraurelia
NCBI Class编号 ncbi_taxonomy_id	5888
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Sodium channel protein type 2 subunit alpha
Molecular weight formula_weight	3370.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KRKQEEVSAIVIQRAYRRYLLKQKVKK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
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	2

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

fit	/app/data/saxs_computation/m5/2m5e/2m5e.fit
pddf	/app/data/pr_computation/m5/2m5e/2m5e.pr.out
profile	/app/data/saxs_computation/m5/2m5e/2m5e.dat

Structure of the C-domain of Calcium-saturated Calmodulin bound to the IQ motif of NaV1.2

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

Calmodulin

State in the Current Structure

Other States of the Same Protein in the Database

Sodium channel protein type 2 subunit alpha

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

6. Entities and Polymers Entities & Polymers (3)

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

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)