SAXSdb — 1t0h

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

VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A

Rattus norvegicus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–145 Chain B； UniProt 203–425	Fragment：residues 17-145 Non-standard monomer：Yes (specific site not provided by mmCIF) Fragment：residues 203-425 Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；281 K；Tris-Cl, NaCl, PEG 4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 1.97 Å R-free 0.213
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–145 Chain B； UniProt 203–425	Fragment：residues 17-145 Non-standard monomer：Yes (specific site not provided by mmCIF) Fragment：residues 203-425 Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；281 K；Tris-Cl, NaCl, PEG 4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 1.97 Å R-free 0.213

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 1T0H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1T0J Crystal structure of a complex between voltage-gated calcium channel beta2a subunit and a peptide of the alpha1c subunit Deposited 2004-04-09	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–145（129 aa） Fragment：residues 17-145 Chain B 203–425（223 aa） Fragment：residues 203-425	Not recorded	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
1T0J Crystal structure of a complex between voltage-gated calcium channel beta2a subunit and a peptide of the alpha1c subunit Deposited 2004-04-09	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–145（129 aa） Fragment：residues 17-145 Chain B 203–425（223 aa） Fragment：residues 203-425	Not recorded	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
3JBR Cryo-EM structure of the rabbit voltage-gated calcium channel Cav1.1 complex at 4.2 angstrom 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 heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 68–196（129 aa） Chain B 254–475（222 aa）	Not recorded	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 BMA beta-D-mannopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer 20mM MOPS, 200mM NaCl, 0.5mM CaCl2,0.1% digitonin；pH 7.4；20mM MOPS, 200mM NaCl, 0.5mM CaCl2,0.1% digitonin cryo-EM vitrification conditions Blot for 2 seconds before plunging；Cryogen ETHANE	Resolution 4.20 Å
5V2P CaV beta2a subunit: CaV1.2 AID-CAP complex Deposited 2017-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–145（122 aa） Fragment：beta2a subunit (UNP residues 24-145,254-476) Chain A 254–476（223 aa） Fragment：beta2a subunit (UNP residues 24-145,254-476)	Not recorded	NI NICKEL (II) ION × 1 1PE PENTAETHYLENE GLYCOL × 2 8VY 1,3-bis(bromomethyl)benzene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；34-37% PEG400, 0.1 M magnesium chloride, 0.1 M MES, pH 6.3	Resolution 2.00 Å R-free 0.230
5V2Q CaV beta2a subunit: CaV1.2 AID-CEN complex Deposited 2017-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 68–189（122 aa） Fragment：beta2a subunit (UNP residues 68-189,203-425) Chain A 203–425（223 aa） Fragment：beta2a subunit (UNP residues 68-189,203-425)	Not recorded	CL CHLORIDE ION × 1 8VY 1,3-bis(bromomethyl)benzene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.5-1.7 M ammonium sulfate, 5 mM BME, 0.1 M HEPES, pH 7.0	Resolution 1.70 Å R-free 0.196

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 2–224； UniProt 203–425

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	1t0h
Deposition date deposition_date	2004-04-08
Structure title title	Crystal structure of the Rattus norvegicus voltage gated calcium channel beta subunit isoform 2a
Keywords keywords	SH3 domain, Nucleotide kinase like domain, SIGNALING PROTEIN; SIGNALING 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	23.32 Å
Radius of gyration Rg (electron density) rg_electron	22.10 Å
Forward intensity I(0) i0	18280800.00
Molecular weight molecular_weight	32018.0 kDa
Excluded volume excluded_volume	39982 Å³
Envelope volume envelope_volume	50847 Å³
Hydration-shell volume shell_volume	20031 Å³
Envelope diameter envelope_diameter	82.8 Å
Shell Rg shell_rg	28.10 Å
Envelope Rg envelope_rg	22.56 Å
Shape Rg shape_rg	22.01 Å
Total Rg total_rg	23.20 Å
Total atoms total_atoms	2229
Residues n_residues	276
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	82.0 Å
Rg (real space) rg_real	23.37 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.8280e+07
I(0) uncertainty (real space) i0_real_error	2.6200e+05
Rg (reciprocal space) rg_reciprocal	23.36 Å
I(0) (reciprocal space) i0_reciprocal	18280000.0000
Solution quality estimate total_estimate	0.6854
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.388
Kurtosis Kurtosis kurtosis	-0.351
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3552000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 0.223; Positv: 1.000; Valcen: 0.887; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
Molecular weight formula_weight	15137.5 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	2377

GHMGSADSYTSRPSDSDVSLEEDREAVRREAERQAQAQLEKAKTKPVAFAVRTNVRYSAAQEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSPVKLENMRLQHEQRAKQGKFYSSKS

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
Molecular weight formula_weight	25602.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSKEKRMPFFKKTEHTPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNNPSKHAIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIIVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPQESFDVILDENQLEDACEHLADYLEAYWKATHPPSSNLPNPLLSRT

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway 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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1t0ha_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d1t0hb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

CATH v4.4 (2 domains)

Domain ID domain_id	1t0hA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	1t0hB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	36.176 Å
Unit-cell length b length_b	45.260 Å
Unit-cell length c length_c	58.701 Å
Unit-cell angle α angle_alpha	107.34 °
Unit-cell angle β angle_beta	95.75 °
Unit-cell angle γ angle_gamma	97.00 °
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	—

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	55.050 Å
R factor r_factor	0.1869
R_work r_work	0.1855
R_free r_free	0.2132

fit	/app/data/saxs_computation/t0/1t0h/1t0h.fit
pddf	/app/data/pr_computation/t0/1t0h/1t0h.pr.out
profile	/app/data/saxs_computation/t0/1t0h/1t0h.dat

Crystal structure of the Rattus norvegicus voltage gated calcium channel beta subunit isoform 2a

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

VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

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 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)