8rkt

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

Method: ELECTRON MICROSCOPY

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

ShCas12k

Scytonema hofmannii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 DNA 2 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand - LE × 1 Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） TniQ × 1 （A0A8J0PCL5） MAGNESIUM ION × 1 ZINC ION × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 DNA 2 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand - LE × 1 ShCas12k × 1 （A0A8X6EH11） TniQ × 1 （A0A8J0PCL5） MAGNESIUM ION × 1 ZINC ION × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 DNA 2 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand - LE × 1 ShCas12k × 1 （A0A8X6EH11） Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） MAGNESIUM ION × 1 ZINC ION × 2 water × 6	Consistent with all polymers

Other States of the Same Protein in the Database

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.

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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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8rkt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8rkt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rkt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.72 Å
Rg (electron density)	38.21 Å
Total Rg	38.64 Å
Atom count	13471
Residues	1165
Excluded volume	216570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rkt__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Scytonema hofmannii
NCBI taxonomy ID ncbi_taxonomy_id	34078
Host organism 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

Source Source

Source organism organism	Scytonema hofmannii
NCBI taxonomy ID ncbi_taxonomy_id	34078
Host organism 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

Source Source

Source organism organism	Scytonema hofmannii
NCBI taxonomy ID ncbi_taxonomy_id	34078
Host organism 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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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Method resolution_method	—
颗粒数 num_particles	144000

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8rkt__assembly_1__model_1

8rkt__assembly_1__model_1 | I(q)

8rkt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. 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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ribosomal subunit protein uS15

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TniQ

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8rkt__assembly_1__model_1

8rkt__assembly_1__model_1 | I(q)

8rkt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. 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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)