SAXSdb — 6cuc

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

Tau-theraphotoxin-Hs1a

Haplopelma schmidti

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 1–79	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition：300 uM [U-13C; U-15N] DkTx, 20 mM sodium phosphate, 10 uM DSS, 0.02 % w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% 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 6CUC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N9Z Solution structure of K1 lobe of double-knot toxin Deposited 2015-12-16	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–42（42 aa） Fragment：K1 domain, UNP residues 1-42	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure ambient NMR sample composition 1 mM K1-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NAJ Solution structure of K2 lobe of double-knot toxin Deposited 2016-01-04	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–75（33 aa） Fragment：K2 domain, UNP residues 43-75	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure ambient NMR sample composition 1 mM K2-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5IRX Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc Deposited 2016-03-14	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 × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	6O8 (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium × 4 6OE (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate × 8 6EU resiniferatoxin × 4 6O9 (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).	Resolution 2.95 Å
7L2M Cryo-EM structure of DkTx/RTX-bound full-length TRPV1 Deposited 2020-12-17	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 × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	6EU resiniferatoxin × 4 NA SODIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
7L2R Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state Deposited 2020-12-17	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 × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 4 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7L2T cryo-EM structure of DkTx-bound minimal TRPV1 in partial open state Deposited 2020-12-17	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 × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 NA SODIUM ION × 1 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
7L2U cryo-EM structure of DkTx-bound minimal TRPV1 in open state Deposited 2020-12-17	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 × 6 PDB declaration: hexameric	Chain E 1–75（75 aa） Chain F 1–75（75 aa）	Not recorded	XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 XKP (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate × 4 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DKTX_HAPSC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–82； UniProt 1–79

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	6cuc
Deposition date deposition_date	2018-03-25
Structure title title	Solution structure of double knot toxin (DkTx)
Keywords keywords	ICK, spider toxin, dktx, trpv1, tarantula, TOXIN; TOXIN
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	21.07 Å
Radius of gyration Rg (electron density) rg_electron	21.20 Å
Forward intensity I(0) i0	466098000.00
Molecular weight molecular_weight	176310.0 kDa
Excluded volume excluded_volume	217800 Å³
Envelope volume envelope_volume	51001 Å³
Hydration-shell volume shell_volume	19891 Å³
Envelope diameter envelope_diameter	84.2 Å
Shell Rg shell_rg	28.43 Å
Envelope Rg envelope_rg	23.16 Å
Shape Rg shape_rg	21.18 Å
Total Rg total_rg	21.46 Å
Total atoms total_atoms	23500
Residues n_residues	1560
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	78.5 Å
Rg (real space) rg_real	21.41 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	4.6610e+08
I(0) uncertainty (real space) i0_real_error	6.9060e+06
Rg (reciprocal space) rg_reciprocal	21.35 Å
I(0) (reciprocal space) i0_reciprocal	466100000.0000
Solution quality estimate total_estimate	0.6223
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	11.6 Å
Skewness Skewness skewness	0.374
Kurtosis Kurtosis kurtosis	-0.910
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	314500.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.025; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.011; Smooth: 0.998

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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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8. Citations (1)

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Description description	Tau-theraphotoxin-Hs1a
Molecular weight formula_weight	9287.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	23500

来源生物 organism	Haplopelma schmidti
通用名 common_name	Chinese bird spider
NCBI Class编号 ncbi_taxonomy_id	29017
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/cu/6cuc/6cuc.fit
pddf	/app/data/pr_computation/cu/6cuc/6cuc.pr.out
profile	/app/data/saxs_computation/cu/6cuc/6cuc.dat

Solution structure of double knot toxin (DkTx)

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

Tau-theraphotoxin-Hs1a

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)