8rkt

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K Cas12k domain local-refinement map

Method: ELECTRON MICROSCOPY D_max: 132.8 Å Quality: GOOD

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

ShCas12k

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 × 3 DNA 2 RNA 1 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 4–641	Not recorded	sgRNA × 1 Non-target strand - LE × 1 Target strand - LE × 1 Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） TniQ × 1 （A0A8J0PCL5） 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

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 8RKT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7PLA Cryo-EM structure of ShCas12k in complex with a sgRNA and a dsDNA target Deposited 2021-08-30	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 1–641（641 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
8BD5 Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric	Chain A 1–641（641 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
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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 32-meric	Chain A 4–641（638 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8X6EH11_9CYAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 61–698； UniProt 4–641

Small ribosomal subunit protein uS15

Scytonema hofmannii

UniProt A0A139X9A4

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 × 3 DNA 2 RNA 1 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain B； UniProt 1–89	Not recorded	sgRNA × 1 Non-target strand - LE × 1 Target strand - LE × 1 ShCas12k × 1 （A0A8X6EH11） TniQ × 1 （A0A8J0PCL5） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8RKT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 32-meric	Chain B 1–89（89 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A139X9A4_9CYAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 2–90； UniProt 1–89

TniQ

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	Other combination Heteromer Protein × 3 DNA 2 RNA 1 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain C； UniProt 1–167	Not recorded	sgRNA × 1 Non-target strand - LE × 1 Target strand - LE × 1 ShCas12k × 1 （A0A8X6EH11） Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8RKT	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 R 1–167（167 aa） Chain S 1–167（167 aa） Chain T 1–167（167 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 oligomeric state Different ligand/ion Different experimental conditions 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 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 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 oligomeric state Different ligand/ion 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

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	6
Chains and sequence ranges	Author chain C； 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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8rkt
Deposition date deposition_date	2023-12-30
Structure title title	Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K Cas12k 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	38.72 Å
Radius of gyration Rg (electron density) rg_electron	38.21 Å
Forward intensity I(0) i0	1093180000.00
Molecular weight molecular_weight	197770.0 kDa
Excluded volume excluded_volume	216570 Å³
Envelope volume envelope_volume	321380 Å³
Hydration-shell volume shell_volume	68319 Å³
Envelope diameter envelope_diameter	140.7 Å
Shell Rg shell_rg	45.35 Å
Envelope Rg envelope_rg	37.84 Å
Shape Rg shape_rg	38.15 Å
Total Rg total_rg	38.64 Å
Total atoms total_atoms	13471
Residues n_residues	1165
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	132.8 Å
Rg (real space) rg_real	38.54 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	1.0930e+09
I(0) uncertainty (real space) i0_real_error	1.7120e+07
Rg (reciprocal space) rg_reciprocal	38.66 Å
I(0) (reciprocal space) i0_reciprocal	1093000000.0000
Solution quality estimate total_estimate	0.8684
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.6 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.281
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	100900000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	sgRNA
Molecular weight formula_weight	84006.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	1
Atom count atom_count	13794

GGAUAUUAAUAGCGCCGCAAUUCAUGCUGCUUGCAGCCUCUGAAUUUUGUUAAAUGAGGGUUAGUUUGACUGUAUAAAUACAGUCUUGCUUUCUGACCCUGGUAGCUGCUCACCCUGAUGCUGCUGUCAAUAGACAGGAUAGGUGCGCUCCCAGCAAUAAGGGCGCGGAUGUACUGCUGUAGUGGCUACUGAAUCACCCCCGAUCAAGGGGGAACCCUCCAAAAGGUGGGUUGAAAGGAGAAGUCAUUUAAUAAGGCCACU

Entity 2 Entity 2 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

GTGAAGGTTCTCTTCAGTATTAATAAGGCCACTGTTAAAACGTACTATATAGACATCTCCACAAAAGG

Entity 3 Entity 3 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 4 Entity 4 polymer

Description description	ShCas12k
Molecular weight formula_weight	79479.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGSSHHHHHHSSGLVPRGSHMASWSHPQFEKGGGSGGGSGGSAWSHPQFEKENLYFQGGSSQITIQARLISFESNRQQLWKLMADLNTPLINELLCQLGQHPDFEKWQQKGKLPSTVVSQLCQPLKTDPRFAGQPSRLYMSAIHIVDYIYKSWLAIQKRLQQQLDGKTRWLEMLNSDAELVELSGDTLEAIRVKAAEILAIAMPASESDSASPKGKKGKKEKKPSSSSPKRSLSKTLFDAYQETEDIKSRSAISYLLKNGCKLTDKEEDSEKFAKRRRQVEIQIQRLTEKLISRMPKGRDLTNAKWLETLLTATTTVAEDNAQAKRWQDILLTRSSSLPFPLVFETNEDMVWSKNQKGRLCVHFNGLSDLIFEVYCGNRQLHWFQRFLEDQQTKRKSKNQHSSGLFTLRNGHLVWLEGEGKGEPWNLHHLTLYCCVDNRLWTEEGTEIVRQEKADEITKFITNMKKKSDLSDTQQALIQRKQSTLTRINNSFERPSQPLYQGQSHILVGVSLGLEKPATVAVVDAIANKVLAYRSIKQLLGDNYELLNRQRRQQQYLSHERHKAQKNFSPNQFGASELGQHIDRLLAKAIVALARTYKAGSIVLPKLGDMREVVQSEIQAIAEQKFPGYIEGQQKYAKQYRVNVHRWSYGRLIQSIQSKAAQTGIVIEEGKQPIRGSPHDKAKELALSAYNLRLTRRS

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 5 Entity 5 polymer

Description description	Small ribosomal subunit protein uS15
Molecular weight formula_weight	10376.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SMALTQERKQEIIVNYQVHETDTGSADVQVAMLTERINRLSLHLQANKKDHSSRRGLLKLIGQRKRLLAYIQKDSREKYQALIGRLGIRG

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	TniQ
Molecular weight formula_weight	20468.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MIEAPDVKPWLFLIKPYEGESLSHFLGRFRRANHLSASGLGTLAGIGAIVARWERFHFNPRPSQQELEAIASVVEVDAQRLAQMLPPAGVGMQHEPIRLCGACYAESPCHRIEWQYKSVWKCDRHQLKILAKCPNCQAPFKMPALWEDGCCHRCRMPFAEMAKLQKVGSEFELENLYFQ

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 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	323

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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	2.35 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	144000

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

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K Cas12k domain local-refinement map

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

ShCas12k

State in the Current Structure

Other States of the Same Protein in the Database

Small ribosomal subunit protein uS15

State in the Current Structure

Other States of the Same Protein in the Database

TniQ

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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)