SAXSdb — 8bd6

▼

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

Cas12k

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	Other combination Heteromer Protein × 10 DNA 4 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain A； UniProt 2–639	Not recorded	sgRNA × 1 DNA target strand × 1 DNA non-target strand × 1 TnsC × 9 （A0A8J0PCL3） DNA × 2 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

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 8BD6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8AXA Cryo-EM structure of shCas12k-sgRNA-dsDNA ternary complex (type V-K CRISPR-associated transposon) Deposited 2022-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–639（639 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting, 4 degrees celcius	Resolution 2.96 Å
8AXB Cryo-EM structure of Cas12k-sgRNA binary complex (type V-K CRISPR-associated transposon) Deposited 2022-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–639（639 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting, 4 degrees celcius	Resolution 2.87 Å
8EA3 V-K CAST Transpososome from Scytonema hofmanni, major configuration Deposited 2022-08-27	Different construct 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 O 1–639（639 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 31-meric	Chain O 1–639（639 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
9GO0 Cryo-EM structure of ShCas12k in complex with a sgRNA and a dsDNA target Deposited 2024-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–639（639 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-KOH pH 7.5, 50 mM KCl, 10 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å

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

View Construct and Data Evidence

UniProt name	A0A8M0FGU0_9CYAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 61–698； UniProt 2–639

TnsC

Scytonema hofmannii

UniProt A0A8J0PCL3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 10 DNA 4 RNA 1 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain R； UniProt 1–276 Chain S； UniProt 1–276 Chain T； UniProt 1–276 Chain U； UniProt 1–276 Chain V； UniProt 1–276 Chain W； UniProt 1–276 Chain X； UniProt 1–276 Chain Y； UniProt 1–276 Chain Z； UniProt 1–276	Not recorded	Cas12k × 1 （A0A8M0FGU0） sgRNA × 1 DNA target strand × 1 DNA non-target strand × 1 DNA × 2 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

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 8BD6	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 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 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
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	5
Chains and sequence ranges	Author chain R； PDBConstruct 1–276； UniProt 1–276 Author chain S； PDBConstruct 1–276； UniProt 1–276 Author chain T； PDBConstruct 1–276； UniProt 1–276 Author chain U； PDBConstruct 1–276； UniProt 1–276 Author chain V； PDBConstruct 1–276； UniProt 1–276 Author chain W； PDBConstruct 1–276； UniProt 1–276 Author chain X； PDBConstruct 1–276； UniProt 1–276 Author chain Y； PDBConstruct 1–276； UniProt 1–276 Author chain Z； PDBConstruct 1–276； UniProt 1–276

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8bd6
Deposition date deposition_date	2022-10-18
Structure title title	Cas12k-sgRNA-dsDNA-TnsC non-productive complex.
Keywords keywords	Cas12k, sgRNA, TnsC, CRISPR-Cas, Tn7-like transposons, transposition, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	55.17 Å
Radius of gyration Rg (electron density) rg_electron	54.30 Å
Forward intensity I(0) i0	3684510000.00
Molecular weight molecular_weight	432650.0 kDa
Excluded volume excluded_volume	510340 Å³
Envelope volume envelope_volume	801510 Å³
Hydration-shell volume shell_volume	120120 Å³
Envelope diameter envelope_diameter	190.1 Å
Shell Rg shell_rg	60.53 Å
Envelope Rg envelope_rg	52.56 Å
Shape Rg shape_rg	54.27 Å
Total Rg total_rg	54.53 Å
Total atoms total_atoms	29951
Residues n_residues	3213
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	187.0 Å
Rg (real space) rg_real	55.09 Å
Rg uncertainty (real space) rg_real_error	1.39 Å
I(0) (real space) i0_real	3.6850e+09
I(0) uncertainty (real space) i0_real_error	7.0140e+07
Rg (reciprocal space) rg_reciprocal	55.22 Å
I(0) (reciprocal space) i0_reciprocal	3685000000.0000
Solution quality estimate total_estimate	0.8764
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.5 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	336500000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.846

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Cas12k
Molecular weight formula_weight	79156.8 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	29951

MGSSHHHHHHSGGGSGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKSGGGENLYFQSNASQITIQARLISFESNRQQLWKLMADLNTPLINELLCQLGQHPDFEKWQQKGKLPSTVVSQLCQPLKTDPRFAGQPSRLYMSAIHIVDYIYKSWLAIQKRLQQQLDGKTRWLEMLNSDAELVELSGDTLEAIRVKAAEILAIAMPASESDSASPKGKKGKKEKKPSSSSPKRSLSKTLFDAYQETEDIKSRSAISYLLKNGCKLTDKEEDSEKFAKRRRQVEIQIQRLTEKLISRMPKGRDLTNAKWLETLLTATTTVAEDNAQAKRWQDILLTRSSSLPFPLVFETNEDMVWSKNQKGRLCVHFNGLSDLIFEVYCGNRQLHWFQRFLEDQQTKRKSKNQHSSGLFTLRNGHLVWLEGEGKGEPWNLHHLTLYCCVDNRLWTEEGTEIVRQEKADEITKFITNMKKKSDLSDTQQALIQRKQSTLTRINNSFERPSQPLYQGQSHILVGVSLGLEKPATVAVVDAIANKVLAYRSIKQLLGDNYELLNRQRRQQQYLSHERHKAQKNFSPNQFGASELGQHIDRLLAKAIVALARTYKAGSIVLPKLGDMREVVQSEIQAIAEQKFPGYIEGQQKYAKQYRVNVHRWSYGRLIQSIQSKAAQTGIVIEEGKQPIRGSPHDKAKELALSAYNLRLTRRS

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	sgRNA
Molecular weight formula_weight	82376.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

GGAUAUUAAUAGCGCCGCAAUUCAUGCUGCUUGCAGCCUCUGAAUUUUGUUAAAUGAGGGUUAGUUUGACUGUAUAAAUACAGUCUUGCUUUCUGACCCUGGUAGCUGCUCACCCUGAUGCUGCUGUCAAUAGACAGGAUAGGUGCGCUCCCAGCAAUAAGGGCGCGGAUGUACUGCUGUAGUGGCUACUGAAUCACCCCCGAUCAAGGGGGAACCCUAAAUGGGUUGAAAGGAGAAGUCAUUUAAUAAGGCCACU

Entity 3 Entity 3 polymer

Description description	DNA target strand
Molecular weight formula_weight	14916.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

ATATCTACGTTTAACAGTGGCCTTATTAAATGACTTCTCAACCTCCTAC

Entity 4 Entity 4 polymer

Description description	DNA non-target strand
Molecular weight formula_weight	15125.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GTAGGAGGTTCTCTTCAGTATTAATAAGGCCACTGTTAAACGTACTATA

Entity 5 Entity 5 polymer

Description description	TnsC
Molecular weight formula_weight	31444.6 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T,U,V,W,X,Y,Z

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 6 Entity 6 polymer

Description description	DNA
Molecular weight formula_weight	12303.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	c,d

ATATATATATATATATATATATATATATATATATATATAT

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	9

▶

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	4.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	133000

fit	/app/data/saxs_computation/bd/8bd6/8bd6.fit
pddf	/app/data/pr_computation/bd/8bd6/8bd6.pr.out
profile	/app/data/saxs_computation/bd/8bd6/8bd6.dat

Cas12k-sgRNA-dsDNA-TnsC non-productive complex.

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

Cas12k

State in the Current Structure

Other States of the Same Protein in the Database

TnsC

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)