SAXSdb — 7t3k

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

CRISPR-associated protein Csy1

Pseudomonas

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	CRISPR type I-F/YPEST-associated protein Csy2 × 2 （B3G161） CRISPR-associated endonuclease Cas6/Csy4 × 2 （Q02MM2） CRISPR type I-F/YPEST-associated protein Csy3 × 12 （A0A444M080） AcrIF24 × 2 RNA (61-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSY1_PSEAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–434； UniProt 1–434 Author chain a； PDBConstruct 1–434； UniProt 1–434

CRISPR type I-F/YPEST-associated protein Csy2

Pseudomonas

UniProt B3G161

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	CRISPR-associated protein Csy1 × 2 （Q02ML9） CRISPR-associated endonuclease Cas6/Csy4 × 2 （Q02MM2） CRISPR type I-F/YPEST-associated protein Csy3 × 12 （A0A444M080） AcrIF24 × 2 RNA (61-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3G161_PSEAI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–327； UniProt 1–327 Author chain b； PDBConstruct 1–327； UniProt 1–327

CRISPR-associated endonuclease Cas6/Csy4

Pseudomonas

UniProt Q02MM2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	CRISPR-associated protein Csy1 × 2 （Q02ML9） CRISPR type I-F/YPEST-associated protein Csy2 × 2 （B3G161） CRISPR type I-F/YPEST-associated protein Csy3 × 12 （A0A444M080） AcrIF24 × 2 RNA (61-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS6_PSEAB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–187； UniProt 1–187 Author chain c； PDBConstruct 1–187； UniProt 1–187

CRISPR type I-F/YPEST-associated protein Csy3

Pseudomonas

UniProt A0A444M080

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	CRISPR-associated protein Csy1 × 2 （Q02ML9） CRISPR type I-F/YPEST-associated protein Csy2 × 2 （B3G161） CRISPR-associated endonuclease Cas6/Csy4 × 2 （Q02MM2） AcrIF24 × 2 RNA (61-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A444M080_PSEAI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 20–360； UniProt 2–342 Author chain E； PDBConstruct 20–360； UniProt 2–342 Author chain F； PDBConstruct 20–360； UniProt 2–342 Author chain G； PDBConstruct 20–360； UniProt 2–342 Author chain H； PDBConstruct 20–360； UniProt 2–342 Author chain I； PDBConstruct 20–360； UniProt 2–342 Author chain d； PDBConstruct 20–360； UniProt 2–342 Author chain e； PDBConstruct 20–360； UniProt 2–342 Author chain f； PDBConstruct 20–360； UniProt 2–342 Author chain g； PDBConstruct 20–360； UniProt 2–342 Author chain h； PDBConstruct 20–360； UniProt 2–342 Author chain i； PDBConstruct 20–360； UniProt 2–342

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	7t3k
Deposition date deposition_date	2021-12-08
Structure title title	Cryo-EM structure of Csy-AcrIF24 dimer
Keywords keywords	Csy, Cascade, CRISPR, anti-CRISPR, AcrIF24, HYDROLASE-RNA complex; HYDROLASE/RNA
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.

7t3k__assembly_1__model_1

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

Download this curve (.dat)

7t3k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7t3k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	70.54 Å
Rg (electron density)	69.98 Å
Total Rg	70.03 Å
Atom count	50614
Residues	6364
Excluded volume	884450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7t3k__assembly_1__model_1`	22-meric （22）	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 (6)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated protein Csy1
Molecular weight formula_weight	49194.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a
Atom count atom_count	50620

MTSPLPTPTWQELRQFIESFIQERLQGKLDKLQPDEDDKRQTLLATHRREAWLADAARRVGQLQLVTHTLKPIHPDARGSNLHSLPQAPGQPGLAGSHELGDRLVSDVVGNAAALDVFKFLSLQYQGKNLLNWLTEDSAEALQALSDNAEQAREWRQAFIGITTVKGAPASHSLAKQLYFPLPGSGYHLLAPLFPTSLVHHVHALLREARFGDAAKAAREARSRQESWPHGFSEYPNLAIQKFGGTKPQNISQLNNERRGENWLLPSLPPNWQRQNVNAPMRHSSVFEHDFGRTPEVSRLTRTLQRFLAKTVHNNLAIRQRRAQLVAQICDEALQYAARLRELEPGWSATPGCQLHDAEQLWLDPLRAQTDETFLQRRLRGDWPAEVGNRFANWLNRAVSSDSQILGSPEAAQWSQELSKELTMFKEILEDERD

Source Source

Source organism organism	Pseudomonas
NCBI taxonomy ID ncbi_taxonomy_id	286
Host organism host_organism	Escherichia

Entity 2 Entity 2 polymer

Description description	CRISPR type I-F/YPEST-associated protein Csy2
Molecular weight formula_weight	36244.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,b

MSVTDPEALLLLPRLSIQNANAISSPLTWGFPSPGAFTGFVHALQRRVGISLDIELDGVGIVCHRFEAQISQPAGKRTKVFNLTRNPLNRDGSTAAIVEEGRAHLEVSLLLGVHGDGLDDHPAQEIARQVQEQAGAMRLAGGSILPWCNERFPAPNAELLMLGGSDEQRRKNQRRLTRRLLPGFALVSREALLQQHLETLRTTLPEATTLDALLDLCRINFEPPATSSEEEASPPDAAWQVRDKPGWLVPIPAGYNALSPLYLPGEVRNARDRETPLRFVENLFGLGEWLSPHRVAALSDLLWYHHAEPDKGLYRWSTPRFVEHAIA

Source Source

Source organism organism	Pseudomonas
NCBI taxonomy ID ncbi_taxonomy_id	286
Host organism host_organism	Escherichia

Entity 3 Entity 3 polymer

Description description	CRISPR-associated endonuclease Cas6/Csy4
Molecular weight formula_weight	21427.5 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,c

MDHYLDIRLRPDPEFPPAQLMSVLFGKLHQALVAQGGDRIGVSFPDLDESRSRLGERLRIHASADDLRALLARPWLEGLRDHLQFGEPAVVPHPTPYRQVSRVQAKSNPERLRRRLMRRHDLSEEEARKRIPDTVARALDLPFVTLRSQSTGQHFRLFIRHGPLQVTAEEGGFTCYGLSKGGFVPWF

Source Source

Source organism organism	Pseudomonas
NCBI taxonomy ID ncbi_taxonomy_id	286
Host organism host_organism	Escherichia

Entity 4 Entity 4 polymer

Description description	CRISPR type I-F/YPEST-associated protein Csy3
Molecular weight formula_weight	39778.6 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,G,H,I,d,e,f,g,h,i

MKSSHHHHHHENLYFQSNASKPILSTASVLAFERKLDPSDALMSAGAWAQRDASQEWPAVTVREKSVRGTISNRLKTKDRDPAKLDASIQSPNLQTVDVANLPSDADTLKVRFTLRVLGGAGTPSACNDAAYRDKLLQTVATYVNDQGFAELARRYAHNLANARFLWRNRVGAEAVEVRINHIRQGEVARAWRFDALAIGLRDFKADAELDALAELIASGLSGSGHVLLEVVAFARIGDGQEVFPSQELILDKGDKKGQKSKTLYSVRDAAAIHSQKIGNALRTIDTWYPDEDGLGPIAVEPYGSVTSQGKAYRQPKQKLDFYTLLDNWVLRDEAPAVEQQHYVIANLIRGGVFGEAEEK

Source Source

Source organism organism	Pseudomonas
NCBI taxonomy ID ncbi_taxonomy_id	286
Host organism host_organism	Escherichia

Entity 5 Entity 5 polymer

Description description	AcrIF24
Molecular weight formula_weight	24995.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K

MNAIHIGPFSITPAARGLHYGGLPHHQWTLYYGPREMAIKTLPDSYTSSEVRDEFSDIIAEFVIDARHRYAPDVLELVNSDGDAVLARVAVSRLPEALSGCIPDDRFPYWLLTASRPRLGLPVTLNEYTALAVELSAPPLAWITGLLPGEVLTHDAEEWRPPTSWELRHVVGEGSFTGVSGAAAAALLGMSATNFRKYTAGDSAANRQKISFAAWHYLLDRLGVKRAS

Source Source

Source organism organism	Pseudomonas
NCBI taxonomy ID ncbi_taxonomy_id	286
Host organism host_organism	Escherichia

Entity 6 Entity 6 polymer

Description description	RNA (61-MER)
Molecular weight formula_weight	19538.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	M,m

CUAAGAAAUUCACGGCGGGCUUGAUGUCCGCGUCUACCUGAUUCACUGCCGUAUAGGCAGC

Source Source

Source organism organism	Pseudomonas
NCBI taxonomy ID ncbi_taxonomy_id	286
Host organism host_organism	Escherichia

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7t3kC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2540 — CRISPR-associated endoribonuclease Cas6/Csy4

Domain ID domain_id	7t3kc01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2540 — CRISPR-associated endoribonuclease Cas6/Csy4

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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	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	58133

Cryo-EM structure of Csy-AcrIF24 dimer

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

CRISPR-associated protein Csy1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRISPR type I-F/YPEST-associated protein Csy2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRISPR-associated endonuclease Cas6/Csy4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRISPR type I-F/YPEST-associated protein Csy3

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

7t3k__assembly_1__model_1

7t3k__assembly_1__model_1 | I(q)

7t3k__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 (6)

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

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)