8ea4

V-K CAST Transpososome from Scytonema hofmanni, minor configuration

Method: ELECTRON MICROSCOPY

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

TnsC

Scytonema hofmannii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 24 DNA 6 RNA 1	Cas12k × 1 （A0A8M0FGU0） TniQ × 1 （A0A8J0PCL5） 30S ribosomal protein S15 × 1 （D8EB41） TnsB × 8 Target-LE × 1 LE_R × 1 Non-target_R × 1 RE_F × 1 RE_R1 × 1 RE_R2 × 1 sg_RNA × 1 MAGNESIUM ION × 15 ADENOSINE-5'-TRIPHOSPHATE × 13	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 1–276 Author chain B； PDBConstruct 1–276； UniProt 1–276 Author chain C； PDBConstruct 1–276； UniProt 1–276 Author chain D； PDBConstruct 1–276； UniProt 1–276 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 Author chain L； PDBConstruct 1–276； UniProt 1–276 Author chain M； PDBConstruct 1–276； UniProt 1–276

Cas12k

Scytonema hofmannii

UniProt A0A8M0FGU0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 24 DNA 6 RNA 1	TnsC × 13 （A0A8J0PCL3） TniQ × 1 （A0A8J0PCL5） 30S ribosomal protein S15 × 1 （D8EB41） TnsB × 8 Target-LE × 1 LE_R × 1 Non-target_R × 1 RE_F × 1 RE_R1 × 1 RE_R2 × 1 sg_RNA × 1 MAGNESIUM ION × 15 ADENOSINE-5'-TRIPHOSPHATE × 13	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

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 24 DNA 6 RNA 1	TnsC × 13 （A0A8J0PCL3） Cas12k × 1 （A0A8M0FGU0） 30S ribosomal protein S15 × 1 （D8EB41） TnsB × 8 Target-LE × 1 LE_R × 1 Non-target_R × 1 RE_F × 1 RE_R1 × 1 RE_R2 × 1 sg_RNA × 1 MAGNESIUM ION × 15 ADENOSINE-5'-TRIPHOSPHATE × 13	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	3
Chains and sequence ranges	Author chain Q； PDBConstruct 1–167； UniProt 1–167

30S ribosomal protein S15

Escherichia coli

UniProt D8EB41

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 24 DNA 6 RNA 1	TnsC × 13 （A0A8J0PCL3） Cas12k × 1 （A0A8M0FGU0） TniQ × 1 （A0A8J0PCL5） TnsB × 8 Target-LE × 1 LE_R × 1 Non-target_R × 1 RE_F × 1 RE_R1 × 1 RE_R2 × 1 sg_RNA × 1 MAGNESIUM ION × 15 ADENOSINE-5'-TRIPHOSPHATE × 13	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D8EB41_ECOLX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain S； 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	8ea4
Deposition date deposition_date	2022-08-27
Structure title title	V-K CAST Transpososome from Scytonema hofmanni, minor configuration
Keywords keywords	DNA BINDING PROTEIN, DNA BINDING PROTEIN-RNA-DNA complex; DNA BINDING PROTEIN/RNA/DNA
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.

8ea4__assembly_1__model_1

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

Download this curve (.dat)

8ea4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ea4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	79.40 Å
Rg (electron density)	78.57 Å
Total Rg	78.57 Å
Atom count	58049
Residues	6370
Excluded volume	998920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ea4__assembly_1__model_1`	31-meric （31）	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 (14)

Entity 1 Entity 1 polymer

Description description	TnsC
Molecular weight formula_weight	31444.6 kDa
Source method src_method	man
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M
Atom count atom_count	58049

MTEAQAIAKQLGGVKPDDEWLQAEIARLKGKSIVPLQQVKTLHDWLDGKRKARKSCRVVGESRTGKTVACDAYRYRHKPQQEAGRPPTVPVVYIRPHQKCGPKDLFKKITEYLKYRVTKGTVSDFRDRTIEVLKGCGVEMLIIDEADRLKPETFADVRDIAEDLGIAVVLVGTDRLDAVIKRDEQVLERFRAHLRFGKLSGEDFKNTVEMWEQMVLKLPVSSNLKSKEMLRILTSATEGYIGRLDEILREAAIRSLSRGLKKIDKAVLQEVAKEYK

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	Cas12k
Molecular weight formula_weight	73280.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MSQITIQARLISFESNRQQLWKLMADLNTPLINELLCQLGQHPDFEKWQQKGKLPSTVVSQLCQPLKTDPRFAGQPSRLYMSAIHIVDYIYKSWLAIQKRLQQQLDGKTRWLEMLNSDAELVELSGDTLEAIRVKAAEILAIAMPASESDSASPKGKKGKKEKKPSSSSPKRSLSKTLFDAYQETEDIKSRSAISYLLKNGCKLTDKEEDSEKFAKRRRQVEIQIQRLTEKLISRMPKGRDLTNAKWLETLLTATTTVAEDNAQAKRWQDILLTRSSSLPFPLVFETNEDMVWSKNQKGRLCVHFNGLSDLIFEVYCGNRQLHWFQRFLEDQQTKRKSKNQHSSGLFTLRNGHLVWLEGEGKGEPWNLHHLTLYCCVDNRLWTEEGTEIVRQEKADEITKFITNMKKKSDLSDTQQALIQRKQSTLTRINNSFERPSQPLYQGQSHILVGVSLGLEKPATVAVVDAIANKVLAYRSIKQLLGDNYELLNRQRRQQQYLSHERHKAQKNFSPNQFGASELGQHIDRLLAKAIVALARTYKAGSIVLPKLGDMREVVQSEIQAIAEQKFPGYIEGQQKYAKQYRVNVHRWSYGRLIQSIQSKAAQTGIVIEEGKQPIRGSPHDKAKELALSAYNLRLTRRS

Source Source

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

Entity 3 Entity 3 polymer

Description description	TniQ
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 4 Entity 4 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	S

MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	TnsB
Molecular weight formula_weight	66637.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,X,Y,Z,w,x,y,z

MNSQQNPDLAVHPLAIPMEGLLGESATTLEKNVIATQLSEEAQVKLEVIQSLLEPCDRTTYGQKLREAAEKLNVSLRTVQRLVKNWEQDGLVGLTQTSRADKGKHRIGEFWENFITKTYKEGNKGSKRMTPKQVALRVEAKARELKDSKPPNYKTVLRVLAPILEKQQKAKSIRSPGWRGTTLSVKTREGKDLSVDYSNHVWQCDHTRVDVLLVDQHGEILSRPWLTTVIDTYSRCIMGINLGFDAPSSGVVALALRHAILPKRYGSEYKLHCEWGTYGKPEHFYTDGGKDFRSNHLSQIGAQLGFVCHLRDRPSEGGVVERPFKTLNDQLFSTLPGYTGSNVQERPEDAEKDARLTLRELEQLLVRYIVDRYNQSIDARMGDQTRFERWEAGLPTVPVPIPERDLDICLMKQSRRTVQRGGCLQFQNLMYRGEYLAGYAGETVNLRFDPRDITTILVYRQENNQEVFLTRAHAQGLETEQLALDEAEAASRRLRTAGKTISNQSLLQEVVDRDALVATKKSRKERQKLEQTVLRSAAVDESNRESLPSQIVEPDEVESTETVHSQYEDIEVWDYEQLREEYGF

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	Target-LE
Molecular weight formula_weight	43440.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	1

GTCACAATGACATTAATCTGTCACCGACGACAGATAATTTGTCACTGTACAGTAGAATATAGATGCGCATCTATATAGATGCAAATTGAGTGGCCTTATTAAATGACTTCTCAACCAGTCAGCACGCCCAGACCAGGGCAC

Entity 7 Entity 7 polymer

Description description	LE_R
Molecular weight formula_weight	15775.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	2

TGTACAGTGACAAATTATCTGTCGTCGGTGACAGATTAATGTCATTGTGAC

Entity 8 Entity 8 polymer

Description description	Non-target_R
Molecular weight formula_weight	21815.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	3

GCGTGCTGACTGGTTCTCTTCAGTATTAATAAGGCCACTCAATTTGCATCTATATAGATGCGCATCTATAT

Entity 9 Entity 9 polymer

Description description	RE_F
Molecular weight formula_weight	23080.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	4

TTACTGATGACAATAATTTGTCACAACGACATATAATTAGTCACTGTACATCTACGATACGTAGCGGCCGACGCG

Entity 10 Entity 10 polymer

Description description	RE_R1
Molecular weight formula_weight	15444.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	5

TGTACAGTGACTAATTATATGTCGTTGTGACAAATTATTGTCATCAGTAA

Entity 11 Entity 11 polymer

Description description	RE_R2
Molecular weight formula_weight	6086.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	6

CGCGTCGGCCGCTACGTATC

Entity 12 Entity 12 polymer

Description description	sg_RNA
Molecular weight formula_weight	85261.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	7

AUAUUAAUAGCGCCGCAAUUCAUGCUGCUUGCAGCCUCUGAAUUUUGUUAAAUGAGGGUUAGUUUGACUGUAUAAAUACAGUCUUGCUUUCUGACCCUGGUAGCUGCUCACCCUGAUGCUGCUGUCAAUAGACAGGAUAGGUGCGCUCCCAGCAAUAAGGGCGCGGAUGUACUGCUGUAGUGGCUACUGAAUCACCCCCGAUCAAGGGGGAACCCUCCAAAAGGUGGGUUGAAAGGAGAAGUCAUUUAAUAAGGCCACUGUUAAA

Entity 13 Entity 13 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 14 Entity 14 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	8ea4D01
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	8ea4H01
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	8ea4I01
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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Resolution resolution	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	67096

V-K CAST Transpososome from Scytonema hofmanni, minor configuration

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

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

Cas12k

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

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

8ea4__assembly_1__model_1

8ea4__assembly_1__model_1 | I(q)

8ea4__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 polymer

Polymer Polymer

Entity 11 Entity 11 polymer

Polymer Polymer

Entity 12 Entity 12 polymer

Polymer Polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)