SAXSdb — 1du1

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

SKELETAL DIHYDROPYRIDINE RECEPTOR

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 671–690	Fragment：II-III LOOP REGION, FRAGMENT THR671-LEU690 A1	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5；278 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition：4 mM peptide, no buffer \| 90% H2O/10% 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 1DU1	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 357–374（18 aa） Fragment：AID	Not recorded	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
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 A 1–1395（1395 aa） Chain A 1521–1873（353 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
5GJV Structure of the mammalian voltage-gated calcium channel Cav1.1 complex at near atomic resolution Deposited 2016-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1873（1873 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；100 mM Tris-HCl, pH 8.0,200 mM NaCl, 10 mM CaCl2,15 mM reduced glutathione, 0.1% digitonin, and protease inhibitors. cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2 s and flash-frozen in liquid ethane cooled by liquid nitrogen	Resolution 3.60 Å
5GJW Structure of the mammalian voltage-gated calcium channel Cav1.1 complex for ClassII map Deposited 2016-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1873（1873 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8；100 mM Tris-HCl, pH 8.0,200 mM NaCl, 10 mM CaCl2,15 mM reduced glutathione, 0.1% digitonin, and protease inhibitors. cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 2 s and flash-frozen in liquid ethane cooled by liquid nitrogen	Resolution 3.90 Å
6BYO Residue assignment correction to the voltage gated calcium Cav1.1 rabbit alpha 1 subunit PDB entries 3JBR & 5GJV Deposited 2017-12-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–1388（1357 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.60 Å
6JP5 Rabbit Cav1.1-Nifedipine Complex Deposited 2019-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1873（1873 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 8 C5U dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ETA ETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6JP8 Rabbit Cav1.1-Bay K8644 Complex Deposited 2019-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1873（1873 aa）	Not recorded	C8U methyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 2 ETA ETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
6JPA Rabbit Cav1.1-Verapamil Complex Deposited 2019-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1506（1506 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 8 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 4YH (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile × 2 ETA ETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
6JPB Rabbit Cav1.1-Diltiazem Complex Deposited 2019-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–1873（1873 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 C9F Diltiazem × 1 ETA ETHANOLAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7JPK Rabbit Cav1.1 in the presence of 100 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.0 Angstrom resolution Deposited 2020-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 C8U methyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 3.00 Å
7JPL Rabbit Cav1.1 in the presence of 10 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.4 Angstrom resolution Deposited 2020-08-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 C8U methyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 3.40 Å
7JPV Rabbit Cav1.1 in the presence of 1 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.4 Angstrom resolution Deposited 2020-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 3.40 Å
7JPW Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2 Angstrom resolution Deposited 2020-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 VFY methyl (4R)-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 3.20 Å
7JPX Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom resolution Deposited 2020-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 9 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 6UB amlodipine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging	Resolution 2.90 Å
7RXQ Crystal structure of junctophilin-2 in complex with a CaV1.1 peptide Deposited 2021-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1594–1609（16 aa） Fragment：EERIFRRTGGLFGQVD correspond to UNP residues 1594-1609	Not recorded	EOH ETHANOL × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG3350, potassium sulphate	Resolution 2.03 Å R-free 0.252
8E56 Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone at 2.8 Angstrom resolution Deposited 2022-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 2 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8E57 Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 100 microM MNI-1 at 2.8 Angstrom resolution Deposited 2022-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 2 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 WFR propan-2-yl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-ethynyl-3-hydroxy-4-methyloxolan-2-yl]methoxy}(phenoxy)phosphoryl]amino}propanoate (non-preferred name) × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8E58 Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 1 mM MNI-1 at 3.0 Angstrom resolution Deposited 2022-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1873（1873 aa）	Not recorded	CA CALCIUM ION × 2 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 WFR propan-2-yl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-ethynyl-3-hydroxy-4-methyloxolan-2-yl]methoxy}(phenoxy)phosphoryl]amino}propanoate (non-preferred name) × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CAC1S_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–20； UniProt 671–690

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	1du1
Deposition date deposition_date	2000-01-13
Structure title title	PEPTIDE FRAGMENT THR671-LEU690 OF THE RABBIT SKELETAL DIHYDROPYRIDINE RECEPTOR
Keywords keywords	DIHYDROPYRIDINE RECEPTOR, RYANODINE RECEPTOR, SIGNALING PROTEIN; SIGNALING PROTEIN
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	10.80 Å
Radius of gyration Rg (electron density) rg_electron	9.84 Å
Forward intensity I(0) i0	198147.00
Molecular weight molecular_weight	2338.0 kDa
Excluded volume excluded_volume	2867 Å³
Envelope volume envelope_volume	3623 Å³
Hydration-shell volume shell_volume	3866 Å³
Envelope diameter envelope_diameter	35.3 Å
Shell Rg shell_rg	13.38 Å
Envelope Rg envelope_rg	10.10 Å
Shape Rg shape_rg	9.76 Å
Total Rg total_rg	11.26 Å
Total atoms total_atoms	343
Residues n_residues	20
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	38.9 Å
Rg (real space) rg_real	10.90 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.9810e+05
I(0) uncertainty (real space) i0_real_error	2.3860e+03
Rg (reciprocal space) rg_reciprocal	10.90 Å
I(0) (reciprocal space) i0_reciprocal	198100.0000
Solution quality estimate total_estimate	0.8361
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	10.3 Å
Skewness Skewness skewness	0.432
Kurtosis Kurtosis kurtosis	-0.374
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16790.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.510; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1du1a_
Class class	j — Peptides
Fold Fold fold	j.68 — Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor)
Superfamily Superfamily superfamily	j.68.1 — Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor)
Family Family family	j.68.1.1 — Fragments of the L-type calcium channel alpha subunit Cav.1 (dihydropyridine receptor)

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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	—

Description description	SKELETAL DIHYDROPYRIDINE RECEPTOR
Molecular weight formula_weight	2339.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	343

fit	/app/data/saxs_computation/du/1du1/1du1.fit
pddf	/app/data/pr_computation/du/1du1/1du1.pr.out
profile	/app/data/saxs_computation/du/1du1/1du1.dat

PEPTIDE FRAGMENT THR671-LEU690 OF THE RABBIT SKELETAL DIHYDROPYRIDINE RECEPTOR

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

SKELETAL DIHYDROPYRIDINE RECEPTOR

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)