9g44

Structure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.

Method: ELECTRON MICROSCOPY

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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 9 DNA 2 RNA 1	CRISPR-associated protein Cas7 × 6 （A4Y6G1） RNA (61-MER) × 1 DNA (39-MER) × 1 DNA (41-MER) × 1 Cas5fv helical domain-containing protein × 1 （A4Y6G2） DEAD-like helicases-like protein × 1 （A4Y6G0） MAGNESIUM ION × 2	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	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–169； UniProt 15–183

CRISPR-associated protein Cas7

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 9 DNA 2 RNA 1	CRISPR-associated protein, Csy4 family × 1 （A4Y6G3） RNA (61-MER) × 1 DNA (39-MER) × 1 DNA (41-MER) × 1 Cas5fv helical domain-containing protein × 1 （A4Y6G2） DEAD-like helicases-like protein × 1 （A4Y6G0） MAGNESIUM ION × 2	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	2
Chains and sequence ranges	Author chain D； PDBConstruct 8–322； UniProt 1–315 Author chain E； PDBConstruct 8–322； UniProt 1–315 Author chain F； PDBConstruct 8–322； UniProt 1–315 Author chain G； PDBConstruct 8–322； UniProt 1–315 Author chain H； PDBConstruct 8–322； UniProt 1–315 Author chain I； PDBConstruct 8–322； UniProt 1–315

Cas5fv helical domain-containing 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 9 DNA 2 RNA 1	CRISPR-associated protein, Csy4 family × 1 （A4Y6G3） CRISPR-associated protein Cas7 × 6 （A4Y6G1） RNA (61-MER) × 1 DNA (39-MER) × 1 DNA (41-MER) × 1 DEAD-like helicases-like protein × 1 （A4Y6G0） MAGNESIUM ION × 2	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	6
Chains and sequence ranges	Author chain B； PDBConstruct 1–336； UniProt 1–336

DEAD-like helicases-like protein

Shewanella putrefaciens CN-32

UniProt A4Y6G0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 9 DNA 2 RNA 1	CRISPR-associated protein, Csy4 family × 1 （A4Y6G3） CRISPR-associated protein Cas7 × 6 （A4Y6G1） RNA (61-MER) × 1 DNA (39-MER) × 1 DNA (41-MER) × 1 Cas5fv helical domain-containing protein × 1 （A4Y6G2） MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4Y6G0_SHEPC
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain A； PDBConstruct 9–882； UniProt 105–978

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	9g44
Deposition date deposition_date	2024-07-13
Structure title title	Structure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.
Keywords keywords	Type I-F2 CRISPR system, Nuclease-Helicase Cas3, Structural characterization, Protein-DNA-RNA complex, Cryo-EM., ANTIVIRAL PROTEIN; ANTIVIRAL 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.

9g44__assembly_1__model_1

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

Download this curve (.dat)

9g44__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9g44__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.60 Å
Rg (electron density)	55.22 Å
Total Rg	55.41 Å
Atom count	28051
Residues	3312
Excluded volume	489980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9g44__assembly_1__model_1`	12-meric （12）	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 (8)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated protein, Csy4 family
Molecular weight formula_weight	19055.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	28051

MREAELSSKVFTKFHKALVTLNSHKIGISFPQMKLSLGQLFRIHGDASLLHDLQGLDWLGPLAGYCQVTAVSAVPDHVQYRIVSVKRSNLSKAKLKRLIARGSIDKDGEKRYKVKMLGQGFDNPYLDLFSSSTGQVYRKFFEFSDIQAHPLDGEFDSYGLSKTATVPWF

Source Source

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

Entity 2 Entity 2 polymer

Description description	CRISPR-associated protein Cas7
Molecular weight formula_weight	36481.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

MGHHHHHMQKVTGIKSVDFKIKALGHGVVNWNGPTTLTGDDGKTVDNHTLPKLRGYTNLTGKVKDETGYKYKKQATDINFKETPLYISQNCIRHHLFREQAFDLHYASDKNLKNVLASITGLIRGYVVPSSQCKRTSPLLLEDFVDQLGNGNFEQYGQAGARDSTSFFSKTTFGDTEYISYGSISIEQLQFISLDKKFDRAAMVIKEGEGEVIAAELQNYIQSLNPSLNPQAIFHSNYVRRGTIFEEGECGILLNDDAVKALVAETLERLANLSIRQAKGYMYVDDITVDYNDSHKMMRIKRDESEIINEQHAPFAQYFYAK

Source Source

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

Entity 3 Entity 3 polymer

Description description	RNA (61-MER)
Molecular weight formula_weight	19531.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	J

CUUAGAAAUAUCGCCCAGCAAGACGCGCAAACCUAUAACCGUUCACCGCCGCACAGGCGGC

Source Source

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

Entity 4 Entity 4 polymer

Description description	DNA (39-MER)
Molecular weight formula_weight	17248.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

CCCACGTGCCACCATCATTATTATTGTTATTATTCTTAGTATTATTCCCCTCCTCGC

Source Source

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

Entity 5 Entity 5 polymer

Description description	DNA (41-MER)
Molecular weight formula_weight	17946.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

GCGAGGAGGGGAGGTTATAGGTTTGCGCGTCTTGCTGGGCGATAGGTGGCACGTGGG

Source Source

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

Entity 6 Entity 6 polymer

Description description	Cas5fv helical domain-containing 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	B

MKIIIEYDSCWRNAFLGGSNNEPVPKKGREFLGSMTSLKKEGNFKVCENTLDTVMGVLNRLIGDQRKLYQARSKMYESAYYFEALEDKVSFIDKPQLTNEISFIRNMNGSTDQNAFTGMIKVSDPVFTSEYSQQFWGVLALDFTQLCDFIIKQSQVVGSIELNPLSIINRLESLNQEKALENSDDLAQVLKVLNEYFPDIEYLNNKGLITPISIYCSALYLQLARLETSFNMTTAKTKAGGISGISKRGFTKKDFMDRYTTGPKKTIWGNPFIKKEKIKGQGEVTSMMTKASGQLEISIDVDRDKAQEIKILIENAGVSSFYLGKKGLAYVSNIKL

Source Source

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

Entity 7 Entity 7 polymer

Description description	DEAD-like helicases-like protein
Molecular weight formula_weight	99727.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGHHHHHHKPKQGVLYANTQLQPLSEHLFAVGFVAELLHRQLFPENTQFSIANFIAGCLHDLGKIQPKFQEWVTNPKKRDFIAEDGQHIDDAKFSFDKHPRHNEVSLLLYQLLDSTELKLLNPSNKRSVKHALYWHHAKPFRKEKNGFDTYKDISKKLVANQKEIGLSDIVGQAQTLLRQVIGIDKKYRELTNRLLEKAFLAEVEQDLEANLPDAPALPSYKEYEFEESVSANSTNVKLNALNNIVRACLISADRTVSALSAAELHTAIFERQLEEIVTELLEVETTLSSDIDTCLNAFFPTSERSQKQRDIAKQLTTAEDVAVLAGAAGCGKTKIALEWAKLQGVKRIIWVCPRVQVCQGLFYELTSEQYLPNSTIEINTGEFKFHNQWDNPIPDDENFSGDIVLTTIDQILGSVISHTKANTLIDFLNVHVVFDEFHEYVNMPAFNLLFAELIAAKKMQKDQAKTLLVSATPHYVFVEDLLGIHPDDIKIMPSFNPSQYQLDFKIFDDTNLSNINPLFAQQSGCTFVISNMALTAQNSFIVNQHNENAVLLHSKFIKSDKRKWFGEVYEAYKRDGTRKYEVLRSGPIVQASLNISCDYMVAEITSAEDCLQRLGRLDRFGENSDVNTYTLAVPESIANGKGKSPAAGFLSKMYALSSVRAWYQFLHSELADKTFTLPEIYQLYFAFHHTERNRGFIASDLVAALKNSVQQINAKVVDPITVPPKNNKDKKRTKISKGSLRGDNRFVQLAVVDLSQAEPKYIEAYAYSIPLDDDSNIDNLTYATKAICGYDQSDKDLLSHMFKKHHNIMGGTGKAFTDKILLNEARDPESPIYLSYTTNDLLQVGGESARHPHAIYYAVCDKQAIGAMSIKQINQTTEDEE

Source Source

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

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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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	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	250975

Structure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.

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

CRISPR-associated protein Cas7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cas5fv helical domain-containing 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

DEAD-like helicases-like 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

9g44__assembly_1__model_1

9g44__assembly_1__model_1 | I(q)

9g44__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 (8)

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

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)