SAXSdb — 9irf

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

CRISPR-associated protein Csy2

Pectobacterium atrosepticum SCRI1043

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	CRISPR-associated endonuclease Cas6f/Csy4 × 1 （Q6D0W5） CRISPR-associated protein Csy3 × 6 （Q6D0W6） crRNA (87-MER) × 1 CRISPR-associated protein Csy1 × 1 （Q6D0W8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSY2_PECAS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 1–310

CRISPR-associated endonuclease Cas6f/Csy4

Pectobacterium atrosepticum SCRI1043

UniProt Q6D0W5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	CRISPR-associated protein Csy2 × 1 （Q6D0W7） CRISPR-associated protein Csy3 × 6 （Q6D0W6） crRNA (87-MER) × 1 CRISPR-associated protein Csy1 × 1 （Q6D0W8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS6_PECAS
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–184； UniProt 1–184

CRISPR-associated protein Csy3

Pectobacterium atrosepticum SCRI1043

UniProt Q6D0W6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	CRISPR-associated protein Csy2 × 1 （Q6D0W7） CRISPR-associated endonuclease Cas6f/Csy4 × 1 （Q6D0W5） crRNA (87-MER) × 1 CRISPR-associated protein Csy1 × 1 （Q6D0W8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSY3_PECAS
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–337； UniProt 1–337 Author chain D； PDBConstruct 1–337； UniProt 1–337 Author chain E； PDBConstruct 1–337； UniProt 1–337 Author chain F； PDBConstruct 1–337； UniProt 1–337 Author chain G； PDBConstruct 1–337； UniProt 1–337 Author chain H； PDBConstruct 1–337； UniProt 1–337

CRISPR-associated protein Csy1

Pectobacterium atrosepticum SCRI1043

UniProt Q6D0W8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 1	CRISPR-associated protein Csy2 × 1 （Q6D0W7） CRISPR-associated endonuclease Cas6f/Csy4 × 1 （Q6D0W5） CRISPR-associated protein Csy3 × 6 （Q6D0W6） crRNA (87-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSY1_PECAS
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain J； PDBConstruct 1–443； UniProt 1–443

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	9irf
Deposition date deposition_date	2024-07-15
Structure title title	Cryo-EM Structure of csy1-4 with crRNA
Keywords keywords	crRNA, cas6f, cas7f, cas5f, cas8f, RNA BINDING PROTEIN/RNA, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/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.

9irf__assembly_1__model_1

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

Download this curve (.dat)

9irf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9irf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.36 Å
Rg (electron density)	49.87 Å
Total Rg	50.07 Å
Atom count	22171
Residues	2736
Excluded volume	387900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9irf__assembly_1__model_1`	decameric （10）	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 (5)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated protein Csy2
Molecular weight formula_weight	34903.4 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	22171

MSTLIILRRIQVENANAIAGLTYGFPAITHFLGFTHALSRKLQASHGLTLEGCGVVSHQHQLHAYGSSWERSFALTRNPLTKEAKTAAFNEEGRMHMTVSLLIRCDGQIPADTTALCEHLKQQAQCQRLAGGTVIDIERVTVQSLPVDEAETRGVMRRLLPGFVLRDRTSLLHRHFQTLQQAKPQAEMIDAWLDFAALKMQAERDPSDETVQWKYLPKPGDGGFLTPLMIGYRAISPLYAPGEVDKTRDPHTPFCFAEAAYGIGEWQGAHRISDISQILWEYDYQNGDYHCRQVADTHSVAEDTSYEFDY

Source Source

Source organism organism	Pectobacterium atrosepticum SCRI1043
NCBI taxonomy ID ncbi_taxonomy_id	218491
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CRISPR-associated endonuclease Cas6f/Csy4
Molecular weight formula_weight	20487.5 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDHYIDIRVQPDPEFTASQLLNALFAKLHRVLGQLANGKIGISFPEVGKTLGECLRLHGTEDALSTLEKTSWLKGLRDYTQVSECKVVPNGVKFRTVRRVQLKSSAERLRRRSVSKGWLTAAEAAARIPDAVEKRSALPFVQIKSLSNGQMFFVFVEHGPLQNAPTAGRFSSYGLSTEATVPWF

Source Source

Source organism organism	Pectobacterium atrosepticum SCRI1043
NCBI taxonomy ID ncbi_taxonomy_id	218491
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	CRISPR-associated protein Csy3
Molecular weight formula_weight	36948.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F,G,H

MAKAATTLKTASVLAFERKLANSDALMYAGNWAQQDNWTAIAIQEKSVRGTISNRLKNALTSDPAKLDAEIQKANLQKVDVAALPFGADTLKIVFTLRVLGNLAQPSVCNDQDYQTALGDIITGYAQEQGFSTLAARYAENIANGRFLWRNRVGAEAIRVVVTKKGERSWEFNGEDYSLRQFSQPAGDLAALTQAIEKGLAGDASALFTVEAYVQLGNGQEVFPSQELVLDEKARNGKSKILYQVNDVAAIHSQKIGNALRTIDDWYPAADEAGPIAVEPYGSVTSRGKAYRQPREKMDFYTLLDNWVIKGDVPMPEQQHYVIATLIRGGVFGEKGE

Source Source

Source organism organism	Pectobacterium atrosepticum SCRI1043
NCBI taxonomy ID ncbi_taxonomy_id	218491
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	crRNA (87-MER)
Molecular weight formula_weight	28060.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

UUCACUGCCGUACAGGCAGCUUAGAAAGCAGAGACUAUCGAUACGGUCUGGACGGAUGCGUUCACUGCCGUACAGGCAGCUUAGAAA

Source Source

Source organism organism	Pectobacterium atrosepticum SCRI1043
NCBI taxonomy ID ncbi_taxonomy_id	218491
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	CRISPR-associated protein Csy1
Molecular weight formula_weight	50453.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MRNGLPEFILSYINNRKQAKLDAFDKEAEKKRATLSGEALSVAELELAKARREIEQKHEVRNWLTDAASRAGQISLVTHALKFTHSDAKGSSVFNAETVEDATTLSTATLAQPAIDAVGNAAALDVAKLLQTEHDGDSLVAALQRGDNRALEALAENPEQLAQWLTGFQQVFTNRQPSSHKLAKQIYFPLANGEYHLLSPLYSSSLAHALHQRISAVRFGDEAKAIRQAQRTNQWHDQLSISYPNLAVQNMGGTKPQNISALNSSRSGRSYLLSSAPPQWNSIEKPPQQHESIFRPRGEVDYHTRATLAQMQRFLLSVKDVENNRDIRQQRLHYLDQLIDQLFFYVASVQNLPVGWSAESELKRAQQLWLDPYRAETDTVFRREREAGDWQQAVAYEFGRWLNRRLKHENLIFGEVERREWSTAALFKRRMREMESALKEELA

Source Source

Source organism organism	Pectobacterium atrosepticum SCRI1043
NCBI taxonomy ID ncbi_taxonomy_id	218491
Host organism host_organism	Escherichia coli

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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	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	71806

Cryo-EM Structure of csy1-4 with crRNA

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

CRISPR-associated protein Csy2

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated endonuclease Cas6f/Csy4

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated protein Csy3

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated protein Csy1

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

9irf__assembly_1__model_1

9irf__assembly_1__model_1 | I(q)

9irf__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 (5)

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

7. Citations (1)

Cryo-EM Structure of csy1-4 with crRNA

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

CRISPR-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 Cas6f/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-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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9irf__assembly_1__model_1

9irf__assembly_1__model_1 | I(q)

9irf__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 (5)

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

7. Citations (1)