SAXSdb — 8rku

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

ShTnsC

Scytonema hofmannii

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–DNA Homooligomer Protein × 14 DNA 2 PDB declaration: 16-meric（16） Consistent with all polymer counts	Chain D； UniProt 2–276 Chain E； UniProt 2–276 Chain F； UniProt 2–276 Chain G； UniProt 2–276 Chain H； UniProt 2–276 Chain I； UniProt 2–276 Chain J； UniProt 2–276 Chain K； UniProt 2–276 Chain L； UniProt 2–276 Chain M； UniProt 2–276 Chain N； UniProt 2–276 Chain O； UniProt 2–276 Chain P； UniProt 2–276 Chain Q； UniProt 2–276	Not recorded	Non-target strand - LE × 1 Target strand - LE × 1 MG MAGNESIUM ION × 14 ATP ADENOSINE-5'-TRIPHOSPHATE × 14	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.30 Å

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 8RKU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8BD4 TniQ-capped Tns-ATP-dsDNA complex Deposited 2022-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 1–276（276 aa） Chain B 1–276（276 aa） Chain C 1–276（276 aa） Chain D 1–276（276 aa） Chain E 1–276（276 aa） Chain F 1–276（276 aa） Chain G 1–276（276 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
8BD5 Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex Deposited 2022-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain E 1–276（276 aa） Chain F 1–276（276 aa） Chain G 1–276（276 aa） Chain H 1–276（276 aa） Chain I 1–276（276 aa） Chain J 1–276（276 aa） Chain K 1–276（276 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8BD6 Cas12k-sgRNA-dsDNA-TnsC non-productive complex. Deposited 2022-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: pentadecameric	Chain R 1–276（276 aa） Chain S 1–276（276 aa） Chain T 1–276（276 aa） Chain U 1–276（276 aa） Chain V 1–276（276 aa） Chain W 1–276（276 aa） Chain X 1–276（276 aa） Chain Y 1–276（276 aa） Chain Z 1–276（276 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 9 MG MAGNESIUM ION × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8EA3 V-K CAST Transpososome from Scytonema hofmanni, major configuration Deposited 2022-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 30-meric	Chain A 1–276（276 aa） Chain B 1–276（276 aa） Chain C 1–276（276 aa） Chain D 1–276（276 aa） Chain E 1–276（276 aa） Chain F 1–276（276 aa） Chain G 1–276（276 aa） Chain H 1–276（276 aa） Chain I 1–276（276 aa） Chain J 1–276（276 aa） Chain K 1–276（276 aa） Chain L 1–276（276 aa）	Not recorded	MG MAGNESIUM ION × 14 ATP ADENOSINE-5'-TRIPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8EA4 V-K CAST Transpososome from Scytonema hofmanni, minor configuration Deposited 2022-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 31-meric	Chain A 1–276（276 aa） Chain B 1–276（276 aa） Chain C 1–276（276 aa） Chain D 1–276（276 aa） Chain E 1–276（276 aa） Chain F 1–276（276 aa） Chain G 1–276（276 aa） Chain H 1–276（276 aa） Chain I 1–276（276 aa） Chain J 1–276（276 aa） Chain K 1–276（276 aa） Chain L 1–276（276 aa） Chain M 1–276（276 aa）	Not recorded	MG MAGNESIUM ION × 15 ATP ADENOSINE-5'-TRIPHOSPHATE × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8RDU Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K composite map Deposited 2023-12-08	Different oligomeric state Different ligand/ion	Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 32-meric	Chain D 2–276（275 aa） Chain E 2–276（275 aa） Chain F 2–276（275 aa） Chain G 2–276（275 aa） Chain H 2–276（275 aa） Chain I 2–276（275 aa） Chain J 2–276（275 aa） Chain K 2–276（275 aa） Chain L 2–276（275 aa） Chain M 2–276（275 aa） Chain N 2–276（275 aa） Chain O 2–276（275 aa） Chain P 2–276（275 aa） Chain Q 2–276（275 aa）	Not recorded	MG MAGNESIUM ION × 17 ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8J0PCL3_9CYAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 2–276； UniProt 2–276 Author chain E； PDBConstruct 2–276； UniProt 2–276 Author chain F； PDBConstruct 2–276； UniProt 2–276 Author chain G； PDBConstruct 2–276； UniProt 2–276 Author chain H； PDBConstruct 2–276； UniProt 2–276 Author chain I； PDBConstruct 2–276； UniProt 2–276 Author chain J； PDBConstruct 2–276； UniProt 2–276 Author chain K； PDBConstruct 2–276； UniProt 2–276 Author chain L； PDBConstruct 2–276； UniProt 2–276 Author chain M； PDBConstruct 2–276； UniProt 2–276 Author chain N； PDBConstruct 2–276； UniProt 2–276 Author chain O； PDBConstruct 2–276； UniProt 2–276 Author chain P； PDBConstruct 2–276； UniProt 2–276 Author chain Q； PDBConstruct 2–276； UniProt 2–276

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	8rku
Deposition date deposition_date	2023-12-30
Structure title title	Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K TnsC domain local-refinement map
Keywords keywords	CRISPR-associated Transposon genome editing transposition, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	48.22 Å
Radius of gyration Rg (electron density) rg_electron	48.09 Å
Forward intensity I(0) i0	2778010000.00
Molecular weight molecular_weight	431380.0 kDa
Excluded volume excluded_volume	537660 Å³
Envelope volume envelope_volume	730490 Å³
Hydration-shell volume shell_volume	118580 Å³
Envelope diameter envelope_diameter	162.6 Å
Shell Rg shell_rg	57.81 Å
Envelope Rg envelope_rg	47.52 Å
Shape Rg shape_rg	48.09 Å
Total Rg total_rg	48.39 Å
Total atoms total_atoms	30188
Residues n_residues	3638
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	150.7 Å
Rg (real space) rg_real	47.82 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	2.7780e+09
I(0) uncertainty (real space) i0_real_error	4.4410e+07
Rg (reciprocal space) rg_reciprocal	48.21 Å
I(0) (reciprocal space) i0_reciprocal	2779000000.0000
Solution quality estimate total_estimate	0.8860
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.9 Å
Skewness Skewness skewness	0.099
Kurtosis Kurtosis kurtosis	-0.488
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0006
Highest regularization parameter α highest_alpha	360100000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.898

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Non-target strand - LE
Molecular weight formula_weight	20961.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	2
Atom count atom_count	30726

GTGAAGGTTCTCTTCAGTATTAATAAGGCCACTGTTAAAACGTACTATATAGACATCTCCACAAAAGG

Entity 2 Entity 2 polymer

Description description	Target strand - LE
Molecular weight formula_weight	40822.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	3

AATTAAATAGTCACAATGACATTAATCTGTCACCGACGACAGATAATTTGTCACTGTACACTACGCCTTTTGTGGAGATGTCTAATATCTACGTTTTAACAGTGGCCTTATTAAATGACTTCTCAACCTTCAC

Entity 3 Entity 3 polymer

Description description	ShTnsC
Molecular weight formula_weight	31400.5 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,G,H,I,J,K,L,M,N,O,P,Q

STEAQAIAKQLGGVKPDDEWLQAEIARLKGKSIVPLQQVKTLHDWLDGKRKARKSCRVVGESRTGKTVACDAYRYRHKPQQEAGRPPTVPVVYIRPHQKCGPKDLFKKITEYLKYRVTKGTVSDFRDRTIEVLKGCGVEMLIIDEADRLKPETFADVRDIAEDLGIAVVLVGTDRLDAVIKRDEQVLERFRAHLRFGKLSGEDFKNTVEMWEQMVLKLPVSSNLKSKEMLRILTSATEGYIGRLDEILREAAIRSLSRGLKKIDKAVLQEVAKEYK

来源 Source

来源生物 organism	Scytonema hofmannii
NCBI Class编号 ncbi_taxonomy_id	34078
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	538

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8. Citations (1)

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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	—

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

Resolution resolution	2.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	258000

fit	/app/data/saxs_computation/rk/8rku/8rku.fit
pddf	/app/data/pr_computation/rk/8rku/8rku.pr.out
profile	/app/data/saxs_computation/rk/8rku/8rku.dat

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K TnsC domain local-refinement map

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

ShTnsC

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)