8bd5

Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex

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 10 DNA 2 RNA 1	sgRNA × 1 DNA target strand × 1 DNA non-target strand × 1 TnsC × 7 （A0A8J0PCL3） TniQ (Homology model) × 1 （A0A8J0PCL5） 30S ribosomal protein S15 × 1 （P0ADZ4） ADENOSINE-5'-TRIPHOSPHATE × 7 MAGNESIUM ION × 7 ZINC ION × 2	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 58–698； UniProt 1–641

TnsC

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 10 DNA 2 RNA 1	ShCas12k × 1 （A0A8X6EH11） sgRNA × 1 DNA target strand × 1 DNA non-target strand × 1 TniQ (Homology model) × 1 （A0A8J0PCL5） 30S ribosomal protein S15 × 1 （P0ADZ4） ADENOSINE-5'-TRIPHOSPHATE × 7 MAGNESIUM ION × 7 ZINC ION × 2	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	5
Chains and sequence ranges	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 Author chain H； PDBConstruct 1–276； UniProt 1–276 Author chain I； PDBConstruct 1–276； UniProt 1–276 Author chain J； PDBConstruct 1–276； UniProt 1–276 Author chain K； PDBConstruct 1–276； UniProt 1–276

TniQ (Homology model)

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 10 DNA 2 RNA 1	ShCas12k × 1 （A0A8X6EH11） sgRNA × 1 DNA target strand × 1 DNA non-target strand × 1 TnsC × 7 （A0A8J0PCL3） 30S ribosomal protein S15 × 1 （P0ADZ4） ADENOSINE-5'-TRIPHOSPHATE × 7 MAGNESIUM ION × 7 ZINC ION × 2	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 Q； PDBConstruct 1–167； UniProt 1–167

30S ribosomal protein S15

Escherichia coli K-12

UniProt P0ADZ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 10 DNA 2 RNA 1	ShCas12k × 1 （A0A8X6EH11） sgRNA × 1 DNA target strand × 1 DNA non-target strand × 1 TnsC × 7 （A0A8J0PCL3） TniQ (Homology model) × 1 （A0A8J0PCL5） ADENOSINE-5'-TRIPHOSPHATE × 7 MAGNESIUM ION × 7 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS15_ECOLI
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain X； PDBConstruct 1–89； UniProt 1–89

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	8bd5
Deposition date deposition_date	2022-10-18
Structure title title	Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex
Keywords keywords	Cas12k, sgRNA, S15, TniQ, TnsC, CRISPR-Cas, Tn7-like transposons, transposition, RNA BINDING PROTEIN; RNA 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.

8bd5__assembly_1__model_1

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

Download this curve (.dat)

8bd5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8bd5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.34 Å
Rg (electron density)	52.95 Å
Total Rg	53.03 Å
Atom count	28398
Residues	2999
Excluded volume	481320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8bd5__assembly_1__model_1`	tridecameric （13）	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 (10)

Entity 1 Entity 1 polymer

Description description	ShCas12k
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	28398

MGSSHHHHHHSGGGSGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKSGGGENLYFQSNASQITIQARLISFESNRQQLWKLMADLNTPLINELLCQLGQHPDFEKWQQKGKLPSTVVSQLCQPLKTDPRFAGQPSRLYMSAIHIVDYIYKSWLAIQKRLQQQLDGKTRWLEMLNSDAELVELSGDTLEAIRVKAAEILAIAMPASESDSASPKGKKGKKEKKPSSSSPKRSLSKTLFDAYQETEDIKSRSAISYLLKNGCKLTDKEEDSEKFAKRRRQVEIQIQRLTEKLISRMPKGRDLTNAKWLETLLTATTTVAEDNAQAKRWQDILLTRSSSLPFPLVFETNEDMVWSKNQKGRLCVHFNGLSDLIFEVYCGNRQLHWFQRFLEDQQTKRKSKNQHSSGLFTLRNGHLVWLEGEGKGEPWNLHHLTLYCCVDNRLWTEEGTEIVRQEKADEITKFITNMKKKSDLSDTQQALIQRKQSTLTRINNSFERPSQPLYQGQSHILVGVSLGLEKPATVAVVDAIANKVLAYRSIKQLLGDNYELLNRQRRQQQYLSHERHKAQKNFSPNQFGASELGQHIDRLLAKAIVALARTYKAGSIVLPKLGDMREVVQSEIQAIAEQKFPGYIEGQQKYAKQYRVNVHRWSYGRLIQSIQSKAAQTGIVIEEGKQPIRGSPHDKAKELALSAYNLRLTRRS

Source Source

Source organism organism	Scytonema hofmannii
NCBI taxonomy ID ncbi_taxonomy_id	34078
Host organism 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	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H,I,J,K

MTEAQAIAKQLGGVKPDDEWLQAEIARLKGKSIVPLQQVKTLHDWLDGKRKARKSCRVVGESRTGKTVACDAYRYRHKPQQEAGRPPTVPVVYIRPHQKCGPKDLFKKITEYLKYRVTKGTVSDFRDRTIEVLKGCGVEMLIIDEADRLKPETFADVRDIAEDLGIAVVLVGTDRLDAVIKRDEQVLERFRAHLRFGKLSGEDFKNTVEMWEQMVLKLPVSSNLKSKEMLRILTSATEGYIGRLDEILREAAIRSLSRGLKKIDKAVLQEVAKEYK

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 (Homology model)
Molecular weight formula_weight	19011.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q

MIEAPDVKPWLFLIKPYEGESLSHFLGRFRRANHLSASGLGTLAGIGAIVARWERFHFNPRPSQQELEAIASVVEVDAQRLAQMLPPAGVGMQHEPIRLCGACYAESPCHRIEWQYKSVWKCDRHQLKILAKCPNCQAPFKMPALWEDGCCHRCRMPFAEMAKLQKV

Source Source

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

Entity 7 Entity 7 polymer

Description description	30S ribosomal protein S15
Molecular weight formula_weight	10290.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 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 9 Entity 9 non-polymer

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

Entity 10 Entity 10 non-polymer

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

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	8bd5E01
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	8bd5F01
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	8bd5G01
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	8bd5H01
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	8bd5I01
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	8bd5J01
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	8bd5K01
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

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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	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	75000

Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex

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

TnsC

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 (Homology model)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S15

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

8bd5__assembly_1__model_1

8bd5__assembly_1__model_1 | I(q)

8bd5__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source 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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)