6qxf

Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system

Method: ELECTRON MICROSCOPY

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

CRISPR-associated protein Csn2

Streptococcus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 20 DNA 2	CRISPR-associated endonuclease Cas1 × 8 （G3ECR2） CRISPR-associated endoribonuclease Cas2 × 4 （G3ECR3） DNA (25-MER) × 1 DNA (25-MER) × 1 CALCIUM ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSN2_STRTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 1–219 Author chain B； PDBConstruct 1–219； UniProt 1–219 Author chain C； PDBConstruct 1–219； UniProt 1–219 Author chain D； PDBConstruct 1–219； UniProt 1–219 Author chain E； PDBConstruct 1–219； UniProt 1–219 Author chain F； PDBConstruct 1–219； UniProt 1–219 Author chain G； PDBConstruct 1–219； UniProt 1–219 Author chain H； PDBConstruct 1–219； UniProt 1–219

CRISPR-associated endonuclease Cas1

Streptococcus thermophilus

UniProt G3ECR2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 20 DNA 2	CRISPR-associated protein Csn2 × 8 （G3ECR4） CRISPR-associated endoribonuclease Cas2 × 4 （G3ECR3） DNA (25-MER) × 1 DNA (25-MER) × 1 CALCIUM ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS1_STRTR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–289； UniProt 1–289 Author chain J； PDBConstruct 1–289； UniProt 1–289 Author chain L； PDBConstruct 1–289； UniProt 1–289 Author chain M； PDBConstruct 1–289； UniProt 1–289 Author chain O； PDBConstruct 1–289； UniProt 1–289 Author chain P； PDBConstruct 1–289； UniProt 1–289 Author chain R； PDBConstruct 1–289； UniProt 1–289 Author chain S； PDBConstruct 1–289； UniProt 1–289

CRISPR-associated endoribonuclease Cas2

Streptococcus thermophilus

UniProt G3ECR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 20 DNA 2	CRISPR-associated protein Csn2 × 8 （G3ECR4） CRISPR-associated endonuclease Cas1 × 8 （G3ECR2） DNA (25-MER) × 1 DNA (25-MER) × 1 CALCIUM ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS2_STRTR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 1–114； UniProt 1–114 Author chain N； PDBConstruct 1–114； UniProt 1–114 Author chain Q； PDBConstruct 1–114； UniProt 1–114 Author chain T； PDBConstruct 1–114； UniProt 1–114

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	6qxf
Deposition date deposition_date	2019-03-07
Structure title title	Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system
Keywords keywords	;CRISPR, Cas, DNA binding, Nuclease, Adaptation, Spacer acquisition, DNA BINDING PROTEIN, Protein complex, Protein-DNA complex, Calcium, Metal-binding, Antiviral ;; DNA BINDING 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.

6qxf__assembly_1__model_1

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

Download this curve (.dat)

6qxf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qxf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	62.70 Å
Rg (electron density)	62.35 Å
Total Rg	62.10 Å
Atom count	34693
Residues	4138
Excluded volume	622660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qxf__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 Csn2
Molecular weight formula_weight	25533.5 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	34693

MKINFSLLDEPMEVNLGTVLVIEDVSVFAQLVKEFYQYDEQSNLTIFDSKIRSIRSSELLLITDILGYDINTSQVLKLLHTDIVSQLNDKPEVRSEIDSLVSLITDIIMAECIENELDIEYDEITLLELIKALGVRIETKSCTVFEKIFEILQIFKYLVKKRILVFVNSLSYFSKDEIYQILEYTKLSQADVLFLEPRQIEGIQQFILDKDYILMPYNN

Source Source

Source organism organism	Streptococcus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	CRISPR-associated endonuclease Cas1
Molecular weight formula_weight	35363.5 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	C-terminal Strep tag
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,L,M,O,P,R,S

MAGWRTVVVNIHSKLSYKNNHLIFRNSYKTEMIHLSEIDILLLETTDIVLTTMLVKRLVDENILVIFCDDKRLPTAFLTPYYARHDSSLQIARQIAWKENVKCEVWTAIIAQKILNQSYYLGECSFFEKSQSIMELYHGLERFDPSNREGHSARIYFNTLFGNDFTRESDNDINAALDYGYTLLLSMFAREVVVCGCMTQIGLKHANQFNQFNLASDIMEPFRPIIDRIVYQNRHNNFVKIKKELFSIFSETYLYNGKEMYLSNIVSDYTKKVIKALNQLGEEIPEFRILESGWSHPQFEKA

Source Source

Source organism organism	Streptococcus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	CRISPR-associated endoribonuclease Cas2
Molecular weight formula_weight	13431.6 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,N,Q,T

MSYRYMRMILMFDMPTDTAEERKAYRKFRKFLLSEGFIMHQFSVYSKLLLNHTANTAMVGRLKANNPKKGNITILTVTEKQFARMIYLYGDKNTSIANSEERLVFLGDNYCDED

Source Source

Source organism organism	Streptococcus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1308
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7559.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X

TTTTTTTTTTTTTTTTTTTTTTTTT

Entity 5 Entity 5 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7785.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

AAAAAAAAAAAAAAAAAAAAAAAAA

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	6qxfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfE02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfF02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfG02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

Domain ID domain_id	6qxfH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11940 —

Domain ID domain_id	6qxfH02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2340 —

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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	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	306470

Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system

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

CRISPR-associated protein Csn2

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated endonuclease Cas1

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated endoribonuclease Cas2

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

6qxf__assembly_1__model_1

6qxf__assembly_1__model_1 | I(q)

6qxf__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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Cas1-Cas2-Csn2-DNA complex from the Type II-A CRISPR-Cas system

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

CRISPR-associated protein Csn2

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 Cas1

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 endoribonuclease Cas2

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

6qxf__assembly_1__model_1

6qxf__assembly_1__model_1 | I(q)

6qxf__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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)