SAXSdb — 8bd4

▼

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

TnsC

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 Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain A； UniProt 1–276 Chain B； UniProt 1–276 Chain C； UniProt 1–276 Chain D； UniProt 1–276 Chain E； UniProt 1–276 Chain F； UniProt 1–276 Chain G； UniProt 1–276	Not recorded	TniQ (Homology model) × 3 （A0A8J0PCL5） ;DNA (5'-D(PGPAPTPCPGPAPTPCPGPAPTPCPGPAPTPC)-3') ; × 2 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

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 8BD4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8BD5 Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex Deposited 2022-10-18	Different oligomeric state Different ligand/ion 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	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
8RKU Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K TnsC domain local-refinement map Deposited 2023-12-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 14 PDB declaration: 16-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 × 14 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 1–276 Author chain B； PDBConstruct 1–276； UniProt 1–276 Author chain C； PDBConstruct 1–276； UniProt 1–276 Author chain D； PDBConstruct 1–276； UniProt 1–276 Author chain E； PDBConstruct 1–276； UniProt 1–276 Author chain F； PDBConstruct 1–276； UniProt 1–276 Author chain G； PDBConstruct 1–276； UniProt 1–276

TniQ (Homology model)

Scytonema hofmannii

UniProt A0A8J0PCL5

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 Heteromer Protein × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain R； UniProt 1–167 Chain S； UniProt 1–167 Chain T； UniProt 1–167	Not recorded	TnsC × 7 （A0A8J0PCL3） ;DNA (5'-D(PGPAPTPCPGPAPTPCPGPAPTPCPGPAPTPC)-3') ; × 2 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

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 8BD4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain Q 1–167（167 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
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 Q 1–167（167 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 Q 1–167（167 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 32-meric	Chain C 1–167（167 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
8RKT Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K Cas12k domain local-refinement map Deposited 2023-12-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: hexameric	Chain C 1–167（167 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8J0PCL5_9CYAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 1–167； UniProt 1–167 Author chain S； PDBConstruct 1–167； UniProt 1–167 Author chain T； PDBConstruct 1–167； UniProt 1–167

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8bd4
Deposition date deposition_date	2022-10-18
Structure title title	TniQ-capped Tns-ATP-dsDNA complex
Keywords keywords	Transposition, TniQ, TnsC, CRISPR-Cas, Tn7-like transposon, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	43.42 Å
Radius of gyration Rg (electron density) rg_electron	43.10 Å
Forward intensity I(0) i0	1174720000.00
Molecular weight molecular_weight	271910.0 kDa
Excluded volume excluded_volume	336190 Å³
Envelope volume envelope_volume	460050 Å³
Hydration-shell volume shell_volume	85171 Å³
Envelope diameter envelope_diameter	131.8 Å
Shell Rg shell_rg	50.97 Å
Envelope Rg envelope_rg	42.52 Å
Shape Rg shape_rg	43.12 Å
Total Rg total_rg	43.37 Å
Total atoms total_atoms	19002
Residues n_residues	2317
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	131.3 Å
Rg (real space) rg_real	43.15 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	1.1750e+09
I(0) uncertainty (real space) i0_real_error	2.0600e+07
Rg (reciprocal space) rg_reciprocal	43.42 Å
I(0) (reciprocal space) i0_reciprocal	1175000000.0000
Solution quality estimate total_estimate	0.8917
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.7 Å
Skewness Skewness skewness	0.088
Kurtosis Kurtosis kurtosis	-0.531
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	71210000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.807

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	TnsC
Molecular weight formula_weight	31444.6 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	19002

MTEAQAIAKQLGGVKPDDEWLQAEIARLKGKSIVPLQQVKTLHDWLDGKRKARKSCRVVGESRTGKTVACDAYRYRHKPQQEAGRPPTVPVVYIRPHQKCGPKDLFKKITEYLKYRVTKGTVSDFRDRTIEVLKGCGVEMLIIDEADRLKPETFADVRDIAEDLGIAVVLVGTDRLDAVIKRDEQVLERFRAHLRFGKLSGEDFKNTVEMWEQMVLKLPVSSNLKSKEMLRILTSATEGYIGRLDEILREAAIRSLSRGLKKIDKAVLQEVAKEYK

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 2 Entity 2 polymer

Description description	TniQ (Homology model)
Molecular weight formula_weight	19011.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T

MIEAPDVKPWLFLIKPYEGESLSHFLGRFRRANHLSASGLGTLAGIGAIVARWERFHFNPRPSQQELEAIASVVEVDAQRLAQMLPPAGVGMQHEPIRLCGACYAESPCHRIEWQYKSVWKCDRHQLKILAKCPNCQAPFKMPALWEDGCCHRCRMPFAEMAKLQKV

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 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPAPTPCPGPAPTPCPGPAPTPCPGPAPTPC)-3') ;
Molecular weight formula_weight	4898.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	U,V

GATCGATCGATCGATC

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

▼

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	8bd4A01
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	8bd4B01
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	8bd4C01
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	8bd4D01
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	8bd4E01
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	8bd4F01
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	8bd4G01
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

▶

8. Citations (1)

▶

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	3.44 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	35964

fit	/app/data/saxs_computation/bd/8bd4/8bd4.fit
pddf	/app/data/pr_computation/bd/8bd4/8bd4.pr.out
profile	/app/data/saxs_computation/bd/8bd4/8bd4.dat

TniQ-capped Tns-ATP-dsDNA complex

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

TnsC

State in the Current Structure

Other States of the Same Protein in the Database

TniQ (Homology model)

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)