SAXSdb — 5o6u

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

CRISPR-associated protein, Csy4 family

Shewanella putrefaciens CN-32

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	crRNA × 1 Uncharacterized protein × 3 （A4Y6G1） Uncharacterized protein × 1 （A4Y6G2） non-target DNA × 1 target DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4Y6G3_SHEPC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–182； UniProt 2–183

Uncharacterized protein

Shewanella putrefaciens CN-32

UniProt A4Y6G1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	crRNA × 1 CRISPR-associated protein, Csy4 family × 1 （A4Y6G3） Uncharacterized protein × 1 （A4Y6G2） non-target DNA × 1 target DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4Y6G1_SHEPC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–315； UniProt 1–315 Author chain D； PDBConstruct 1–315； UniProt 1–315 Author chain E； PDBConstruct 1–315； UniProt 1–315

Uncharacterized protein

Shewanella putrefaciens CN-32

UniProt A4Y6G2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 DNA 2 RNA 1	crRNA × 1 CRISPR-associated protein, Csy4 family × 1 （A4Y6G3） Uncharacterized protein × 3 （A4Y6G1） non-target DNA × 1 target DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4Y6G2_SHEPC
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–336； UniProt 1–336

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	5o6u
Deposition date deposition_date	2017-06-07
Structure title title	Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens
Keywords keywords	RNA SURVEILLANCE, ADAPTIVE IMMUNITY, CRISPR, CASCADE, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

5o6u__assembly_1__model_1

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

Download this curve (.dat)

5o6u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5o6u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.70 Å
Rg (electron density)	41.46 Å
Total Rg	41.68 Å
Atom count	13131
Residues	1506
Excluded volume	227560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5o6u__assembly_1__model_1`	octameric （8）	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	crRNA
Molecular weight formula_weight	13756.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	13131

CUUAGAAAGCAAACCUAUAACCGUUCACCGCCGCACAGGCGGC

Source Source

Source organism organism	Shewanella putrefaciens CN-32
NCBI taxonomy ID ncbi_taxonomy_id	319224
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	CRISPR-associated protein, Csy4 family
Molecular weight formula_weight	20573.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NSYIDIRLKPDAEMREAELSSKVFTKFHKALVTLNSHKIGISFPQMKLSLGQLFRIHGDASLLHDLQGLDWLGPLAGYCQVTAVSAVPDHVQYRIVSVKRSNLSKAKLKRLIARGSIDKDGEKRYKVKMLGQGFDNPYLDLFSSSTGQVYRKFFEFSDIQAHPLDGEFDSYGLSKTATVPWF

Source Source

Source organism organism	Shewanella putrefaciens CN-32
NCBI taxonomy ID ncbi_taxonomy_id	319224
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	35602.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MQKVTGIKSVDFKIKALGHGVVNWNGPTTLTGDDGKTVDNHTLPKLRGYTNLTGKVKDETGYKYKKQATDINFKETPLYISQNCIRHHLFREQAFDLHYASDKNLKNVLASITGLIRGYVVPSSQCKRTSPLLLEDFVDQLGNGNFEQYGQAGARDSTSFFSKTTFGDTEYISYGSISIEQLQFISLDKKFDRAAMVIKEGEGEVIAAELQNYIQSLNPSLNPQAIFHSNYVRRGTIFEEGECGILLNDDAVKALVAETLERLANLSIRQAKGYMYVDDITVDYNDSHKMMRIKRDESEIINEQHAPFAQYFYAK

Source Source

Source organism organism	Shewanella putrefaciens CN-32
NCBI taxonomy ID ncbi_taxonomy_id	319224
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	37904.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MKIIIEYDSCWRNAFLGGSNNEPVPKKGREFLGSMTSLKKEGNFKVCENTLDTVMGVLNRLIGDQRKLYQARSKMYESAYYFEALEDKVSFIDKPQLTNEISFIRNMNGSTDQNAFTGMIKVSDPVFTSEYSQQFWGVLALDFTQLCDFIIKQSQVVGSIELNPLSIINRLESLNQEKALENSDDLAQVLKVLNEYFPDIEYLNNKGLITPISIYCSALYLQLARLETSFNMTTAKTKAGGISGISKRGFTKKDFMDRYTTGPKKTIWGNPFIKKEKIKGQGEVTSMMTKASGQLEISIDVDRDKAQEIKILIENAGVSSFYLGKKGLAYVSNIKL

Source Source

Source organism organism	Shewanella putrefaciens CN-32
NCBI taxonomy ID ncbi_taxonomy_id	319224
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	non-target DNA
Molecular weight formula_weight	6310.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

CCCGGCCCCGTCCATTATTAT

Source Source

Source organism organism	Shewanella putrefaciens CN-32
NCBI taxonomy ID ncbi_taxonomy_id	319224
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	target DNA
Molecular weight formula_weight	8485.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GGTTATAGGTTTGCGGACGGGGCCGGG

Source Source

Source organism organism	Shewanella putrefaciens CN-32
NCBI taxonomy ID ncbi_taxonomy_id	319224
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5o6uB00
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	143.316 Å
Unit-cell length b length_b	143.316 Å
Unit-cell length c length_c	172.698 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	46.911 Å
R factor r_factor	0.2540
R_work r_work	0.2523
R_free r_free	0.2856

Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens

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

CRISPR-associated protein, Csy4 family

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Uncharacterized protein

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

5o6u__assembly_1__model_1

5o6u__assembly_1__model_1 | I(q)

5o6u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)