8rdu

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K composite 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 25 DNA 6 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand -LE × 1 LE × 1 RE × 1 Non-target strand - RE × 1 Target strand × 1 Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） TniQ × 1 （A0A8J0PCL5） ShTnsC × 14 （A0A8J0PCL3） TnsB × 8 （A0A979HMQ2） MAGNESIUM ION × 17 ZINC ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 14 water × 21	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	8
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 25 DNA 6 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand -LE × 1 LE × 1 RE × 1 Non-target strand - RE × 1 Target strand × 1 ShCas12k × 1 （A0A8X6EH11） TniQ × 1 （A0A8J0PCL5） ShTnsC × 14 （A0A8J0PCL3） TnsB × 8 （A0A979HMQ2） MAGNESIUM ION × 17 ZINC ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 14 water × 21	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	9
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 25 DNA 6 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand -LE × 1 LE × 1 RE × 1 Non-target strand - RE × 1 Target strand × 1 ShCas12k × 1 （A0A8X6EH11） Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） ShTnsC × 14 （A0A8J0PCL3） TnsB × 8 （A0A979HMQ2） MAGNESIUM ION × 17 ZINC ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 14 water × 21	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	10
Chains and sequence ranges	Author chain C； PDBConstruct 1–167； UniProt 1–167

ShTnsC

Scytonema hofmannii

UniProt A0A8J0PCL3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 25 DNA 6 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand -LE × 1 LE × 1 RE × 1 Non-target strand - RE × 1 Target strand × 1 ShCas12k × 1 （A0A8X6EH11） Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） TniQ × 1 （A0A8J0PCL5） TnsB × 8 （A0A979HMQ2） MAGNESIUM ION × 17 ZINC ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 14 water × 21	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J0PCL3_9CYAN
Isoform	—
PDB entities	11
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

TnsB

Scytonema hofmannii

UniProt A0A979HMQ2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 25 DNA 6 RNA 1	sgRNA × 1 Non-target strand - LE × 1 Target strand -LE × 1 LE × 1 RE × 1 Non-target strand - RE × 1 Target strand × 1 ShCas12k × 1 （A0A8X6EH11） Small ribosomal subunit protein uS15 × 1 （A0A139X9A4） TniQ × 1 （A0A8J0PCL5） ShTnsC × 14 （A0A8J0PCL3） MAGNESIUM ION × 17 ZINC ION × 2 ADENOSINE-5'-TRIPHOSPHATE × 14 water × 21	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A979HMQ2_9CYAN
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain R； PDBConstruct 2–584； UniProt 2–584 Author chain S； PDBConstruct 2–584； UniProt 2–584 Author chain T； PDBConstruct 2–584； UniProt 2–584 Author chain U； PDBConstruct 2–584； UniProt 2–584 Author chain r； PDBConstruct 2–584； UniProt 2–584 Author chain s； PDBConstruct 2–584； UniProt 2–584 Author chain t； PDBConstruct 2–584； UniProt 2–584 Author chain u； PDBConstruct 2–584； UniProt 2–584

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	8rdu
Deposition date deposition_date	2023-12-08
Structure title title	Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K composite 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.

8rdu__assembly_1__model_1

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

Download this curve (.dat)

8rdu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rdu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	81.44 Å
Rg (electron density)	80.47 Å
Total Rg	80.49 Å
Atom count	60568
Residues	6629
Excluded volume	1041900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rdu__assembly_1__model_1`	32-meric （32）	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 (16)

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	61430

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	LE
Molecular weight formula_weight	23238.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	4

AAAAAAAAAAAAAAATGTACAGTGACAAATTATCTGTCGTCGGTGACAGATTAATGTCATTGTGACTATTTAATT

Entity 5 Entity 5 polymer

Description description	RE
Molecular weight formula_weight	22876.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	5

AAAAAAAAAAAAAAATGTACAGTGACTAATTATATGTCGTTGTGACAAATTATTGTCATCAGTAAAATCCTTAT

Entity 6 Entity 6 polymer

Description description	Non-target strand - RE
Molecular weight formula_weight	24402.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	6

ATAAGGATTTTACTGATGACAATAATTTGTCACAACGACATATAATTAGTCACTGTACACGTAGAGACGTAGCAATGCT

Entity 7 Entity 7 polymer

Description description	Target strand
Molecular weight formula_weight	4560.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	7

AGCATTGCTACGTCT

Entity 8 Entity 8 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 9 Entity 9 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 10 Entity 10 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 11 Entity 11 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

Source Source

Source organism organism	Scytonema hofmannii
NCBI taxonomy ID ncbi_taxonomy_id	34078
Host organism host_organism	Escherichia coli

Entity 12 Entity 12 polymer

Description description	TnsB
Molecular weight formula_weight	66592.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T,U,r,s,t,u

SNSQQNPDLAVHPLAIPMEGLLGESATTLEKNVIATQLSEEAQVKLEVIQSLLEPCDRTTYGQKLREAAEKLNVSLRTVQRLVKNWEQDGLVGLTQTSRADKGKHRIGEFWENFITKTYKEGNKGSKRMTPKQVALRVEAKARELKDSKPPNYKTVLRVLAPILEKQQKAKSIRSPGWRGTTLSVKTREGKDLSVDYSNHVWQCDHTRVDVLLVDQHGEILSRPWLTTVIDTYSRCIMGINLGFDAPSSGVVALALRHAILPKRYGSEYKLHCEWGTYGKPEHFYTDGGKDFRSNHLSQIGAQLGFVCHLRDRPSEGGVVERPFKTLNDQLFSTLPGYTGSNVQERPEDAEKDARLTLRELEQLLVRYIVDRYNQSIDARMGDQTRFERWEAGLPTVPVPIPERDLDICLMKQSRRTVQRGGCLQFQNLMYRGEYLAGYAGETVNLRFDPRDITTILVYRQENNQEVFLTRAHAQGLETEQLALDEAEAASRRLRTAGKTISNQSLLQEVVDRDALVATKKSRKERQKLEQTVLRSAAVDESNRESLPSQIVEPDEVESTETVHSQYEDIEVWDYEQLREEYGF

Source Source

Source organism organism	Scytonema hofmannii
NCBI taxonomy ID ncbi_taxonomy_id	34078
Host organism host_organism	Escherichia coli

Entity 13 Entity 13 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	17

Entity 14 Entity 14 non-polymer

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

Entity 15 Entity 15 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 16 Entity 16 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	862

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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Method resolution_method	—
颗粒数 num_particles	258000

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K composite 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

ShTnsC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TnsB

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

8rdu__assembly_1__model_1

8rdu__assembly_1__model_1 | I(q)

8rdu__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 (16)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

Source Source

Entity 10 Entity 10 polymer

Polymer Polymer

Source Source

Entity 11 Entity 11 polymer

Polymer Polymer

Source Source

Entity 12 Entity 12 polymer

Polymer Polymer