SAXSdb — 4dex

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

Voltage-dependent L-type calcium channel subunit beta-2

Oryctolagus cuniculus

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 51–163 Chain A； UniProt 229–448	Not recorded	Voltage-dependent N-type calcium channel subunit alpha-1B × 1 （Q02294）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；292 K；0.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 , pH 8.0, VAPOR DIFFUSION, temperature 292K X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；292 K；0.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 Soaked with NaBr before freezing, pH 8.0, VAPOR DIFFUSION, temperature 292K X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；292 K；0.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 Soaked with NaBr before freezing, pH 8.0, VAPOR DIFFUSION, temperature 292K	Resolution 2.00 Å R-free 0.238

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 4DEX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1T3L Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core in Complex with Alpha1 Interaction Domain Deposited 2004-04-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–422（398 aa） Fragment：Functional Core (Residues 25-422)	Mutation：P122R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；PEG 20K, Bicine, sodium chloride, beta-mercaptoethanol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.282
1T3S Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core Deposited 2004-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–137（113 aa） Fragment：Functional Core (Residues 25-422) Chain A 203–422（220 aa） Fragment：Functional Core (Residues 25-422)	Mutation：P122R Mutation：P122R	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；292 K；PEG 20K, BICINE, SODIUM CHLORIDE, BETA-MERCAPTOETHANOL, MPD, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.30 Å R-free 0.277
4DEY Crystal structure of the Voltage Dependent Calcium Channel beta-2 Subunit in Complex With The CaV1.2 I-II Linker. Deposited 2012-01-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–163（113 aa） Chain A 229–448（220 aa）	Not recorded	BR BROMIDE ION × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；1.1-1.25 M potassium sodium tartrate, 0.1 M Tris Soaked with KI before freezing , pH 7.5, VAPOR DIFFUSION, temperature 292K X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；1.1-1.25 M potassium sodium tartrate, 0.1 M Tris Soaked with KI before freezing, pH 7.5, VAPOR DIFFUSION, temperature 292K X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；1.1-1.25 M potassium sodium tartrate, 0.1 M Tris Soaked with NaBr before freezing, pH 7.5, VAPOR DIFFUSION, temperature 292K	Resolution 1.95 Å R-free 0.229

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CACB2_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–115； UniProt 51–163 Author chain A； PDBConstruct 120–339； UniProt 229–448

Voltage-dependent N-type calcium channel subunit alpha-1B

Rattus norvegicus

UniProt Q02294

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 358–468	Fragment：Intracellular I-II linker	Voltage-dependent L-type calcium channel subunit beta-2 × 1 （P54288）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；292 K；0.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 , pH 8.0, VAPOR DIFFUSION, temperature 292K X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；292 K；0.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 Soaked with NaBr before freezing, pH 8.0, VAPOR DIFFUSION, temperature 292K X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；292 K；0.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 Soaked with NaBr before freezing, pH 8.0, VAPOR DIFFUSION, temperature 292K	Resolution 2.00 Å R-free 0.238

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	CAC1B_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–113； UniProt 358–468

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	4dex
Deposition date deposition_date	2012-01-22
Structure title title	Crystal structure of the Voltage Dependent Calcium Channel beta-2 Subunit in Complex With The CaV2.2 I-II Linker.
Keywords keywords	MAGUK, Voltage Dependent Calcium Channel, TRANSPORT PROTEIN; TRANSPORT 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	26.16 Å
Radius of gyration Rg (electron density) rg_electron	25.22 Å
Forward intensity I(0) i0	24175800.00
Molecular weight molecular_weight	37815.0 kDa
Excluded volume excluded_volume	47535 Å³
Envelope volume envelope_volume	62785 Å³
Hydration-shell volume shell_volume	22084 Å³
Envelope diameter envelope_diameter	98.2 Å
Shell Rg shell_rg	30.51 Å
Envelope Rg envelope_rg	26.14 Å
Shape Rg shape_rg	25.21 Å
Total Rg total_rg	25.92 Å
Total atoms total_atoms	2664
Residues n_residues	334
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	93.0 Å
Rg (real space) rg_real	26.34 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	2.4180e+07
I(0) uncertainty (real space) i0_real_error	4.0610e+05
Rg (reciprocal space) rg_reciprocal	26.28 Å
I(0) (reciprocal space) i0_reciprocal	24170000.0000
Solution quality estimate total_estimate	0.8399
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.509
Kurtosis Kurtosis kurtosis	-0.245
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3573000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.996

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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	Voltage-dependent L-type calcium channel subunit beta-2
Molecular weight formula_weight	38425.0 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	2826

GSSRPSDSDVSLEEDREAVRREAERQAQAQLEKAKTKPVAFAVRTNVSYSAAHEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSPVKLENMRLQHEQRAKEFKLHSKEKRMPFFKKTEHTPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNNPSKHAIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIVVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPELFDVILDENQLEDACEHLADYLEAYWKATHPPSSNLPNPLL

来源 Source

来源生物 organism	Oryctolagus cuniculus
通用名 common_name	European rabbit,Japanese white rabbit,domestic rabbit,rabbits
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Voltage-dependent N-type calcium channel subunit alpha-1B
Molecular weight formula_weight	13118.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSEFAKERERVENRRAFLKLRRQQQIERELNGYLEWIFKAEEVMLAEEDKNAEEKSPLDAVLKRAATKKSRNDLIHAEEGEDRFVDLCAAGSPFARASLKSGKTESSSYFRRK

来源 Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	162

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4dexa1
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	d4dexa2
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 (3 domains)

Domain ID domain_id	4dexA01
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	4dexA02
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

Domain ID domain_id	4dexB00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2500 —

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8. Citations (1)

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Unit-cell length a length_a	36.908 Å
Unit-cell length b length_b	68.661 Å
Unit-cell length c length_c	79.158 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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	27.313 Å
R factor r_factor	0.1996
R_work r_work	0.1975
R_free r_free	0.2381

fit	/app/data/saxs_computation/de/4dex/4dex.fit
pddf	/app/data/pr_computation/de/4dex/4dex.pr.out
profile	/app/data/saxs_computation/de/4dex/4dex.dat

Crystal structure of the Voltage Dependent Calcium Channel beta-2 Subunit in Complex With The CaV2.2 I-II Linker.

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

Voltage-dependent L-type calcium channel subunit beta-2

State in the Current Structure

Other States of the Same Protein in the Database

Voltage-dependent N-type calcium channel subunit alpha-1B

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 (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 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)