9q85

PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system

Method: ELECTRON MICROSCOPY

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

CRISPR-associated endonuclease Cas9

Streptococcus thermophilus DGCC 7710

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 2 RNA 2	crRNA × 1 tracrRNA × 1 DNA (43-MER) × 1 DNA (43-MER) × 1 CRISPR-associated endonuclease Cas1 × 2 （G3ECR2） CRISPR-associated endoribonuclease Cas2 × 1 （G3ECR3） CRISPR-associated protein Csn2 × 4 （G3ECR4） CALCIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS9_STRTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1388； UniProt 22–1409

CRISPR-associated endonuclease Cas1

Streptococcus thermophilus DGCC 7710

UniProt G3ECR2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 2 RNA 2	CRISPR-associated endonuclease Cas9 × 1 （G3ECR1） crRNA × 1 tracrRNA × 1 DNA (43-MER) × 1 DNA (43-MER) × 1 CRISPR-associated endoribonuclease Cas2 × 1 （G3ECR3） CRISPR-associated protein Csn2 × 4 （G3ECR4） CALCIUM ION × 1	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	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–288； UniProt 1–288 Author chain G； PDBConstruct 1–288； UniProt 1–288

CRISPR-associated endoribonuclease Cas2

Streptococcus thermophilus DGCC 7710

UniProt G3ECR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 2 RNA 2	CRISPR-associated endonuclease Cas9 × 1 （G3ECR1） crRNA × 1 tracrRNA × 1 DNA (43-MER) × 1 DNA (43-MER) × 1 CRISPR-associated endonuclease Cas1 × 2 （G3ECR2） CRISPR-associated protein Csn2 × 4 （G3ECR4） CALCIUM ION × 1	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	7
Chains and sequence ranges	Author chain I； PDBConstruct 1–114； UniProt 1–114

CRISPR-associated protein Csn2

Streptococcus thermophilus DGCC 7710

UniProt G3ECR4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 2 RNA 2	CRISPR-associated endonuclease Cas9 × 1 （G3ECR1） crRNA × 1 tracrRNA × 1 DNA (43-MER) × 1 DNA (43-MER) × 1 CRISPR-associated endonuclease Cas1 × 2 （G3ECR2） CRISPR-associated endoribonuclease Cas2 × 1 （G3ECR3） CALCIUM ION × 1	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	8
Chains and sequence ranges	Author chain L； PDBConstruct 17–235； UniProt 1–219 Author chain M； PDBConstruct 17–235； UniProt 1–219 Author chain N； PDBConstruct 17–235； UniProt 1–219 Author chain O； PDBConstruct 17–235； UniProt 1–219

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	9q85
Deposition date deposition_date	2025-02-22
Structure title title	PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system
Keywords keywords	CIRSPR-Cas, spacer acquisition, Csn2, Cas1, Cas2, CRISPR integrase, DNA BINDING PROTEIN; 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.

9q85__assembly_1__model_1

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

Download this curve (.dat)

9q85__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9q85__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.38 Å
Rg (electron density)	51.66 Å
Total Rg	51.71 Å
Atom count	23106
Residues	2886
Excluded volume	397370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9q85__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 (9)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated endonuclease Cas9
Molecular weight formula_weight	162498.5 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	A
Atom count atom_count	23106

MTKPYSIGLDIGTNSVGWAVITDNYKVPSKKMKVLGNTSKKYIKKNLLGVLLFDSGITAEGRRLKRTARRRYTRRRNRILYLQEIFSTEMATLDDAFFQRLDDSFLVPDDKRDSKYPIFGNLVEEKVYHDEFPTIYHLRKYLADSTKKADLRLVYLALAHMIKYRGHFLIEGEFNSKNNDIQKNFQDFLDTYNAIFESDLSLENSKQLEEIVKDKISKLEKKDRILKLFPGEKNSGIFSEFLKLIVGNQADFRKCFNLDEKASLHFSKESYDEDLETLLGYIGDDYSDVFLKAKKLYDAILLSGFLTVTDNETEAPLSSAMIKRYNEHKEDLALLKEYIRNISLKTYNEVFKDDTKNGYAGYIDGKTNQEDFYVYLKNLLAEFEGADYFLEKIDREDFLRKQRTFDNGSIPYQIHLQEMRAILDKQAKFYPFLAKNKERIEKILTFRIPYYVGPLARGNSDFAWSIRKRNEKITPWNFEDVIDKESSAEAFINRMTSFDLYLPEEKVLPKHSLLYETFNVYNELTKVRFIAESMRDYQFLDSKQKKDIVRLYFKDKRKVTDKDIIEYLHAIYGYDGIELKGIEKQFNSSLSTYHDLLNIINDKEFLDDSSNEAIIEEIIHTLTIFEDREMIKQRLSKFENIFDKSVLKKLSRRHYTGWGKLSAKLINGIRDEKSGNTILDYLIDDGISNRNFMQLIHDDALSFKKKIQKAQIIGDEDKGNIKEVVKSLPGSPAIKKGILQSIKIVDELVKVMGGRKPESIVVEMARENQYTNQGKSNSQQRLKRLEKSLKELGSKILKENIPAKLSKIDNNALQNDRLYLYYLQNGKDMYTGDDLDIDRLSNYDIDHIIPQAFLKDNSIDNKVLVSSASNRGKSDDFPSLEVVKKRKTFWYQLLKSKLISQRKFDNLTKAERGGLLPEDKAGFIQRQLVETRQITKHVARLLDEKFNNKKDENNRAVRTVKIITLKSTLVSQFRKDFELYKVREINDFHHAHDAYLNAVIASALLKKYPKLEPEFVYGDYPKYNSFRERKSATEKVYFYSNIMNIFKKSISLADGRVIERPLIEVNEETGESVWNKESDLATVRRVLSYPQVNVVKKVEEQNHGLDRGKPKGLFNANLSSKPKPNSNENLVGAKEYLDPKKYGGYAGISNSFAVLVKGTIEKGAKKKITNVLEFQGISILDRINYRKDKLNFLLEKGYKDIELIIELPKYSLFELSDGSRRMLASILSTNNKRGEIHKGNQIFLSQKFVKLLYHAKRISNTINENHRKYVENHKKEFEELFYYILEFNENYVGAKKNGKLLNSAFQSWQNHSIDELCSSFIGPTGSERKGLFELTSRGSAADFEFLGVKIPRYRDYTPSSLLKDATLIHQSVTGLYETRIDLAKLGEGLEGHHHHHH

Source Source

Source organism organism	Streptococcus thermophilus DGCC 7710
NCBI taxonomy ID ncbi_taxonomy_id	1268061
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	crRNA
Molecular weight formula_weight	13609.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

CGCUAAAGAGGAAGAGGACAGUUUUAGAGCUGUGUUGUUUCG

Entity 3 Entity 3 polymer

Description description	tracrRNA
Molecular weight formula_weight	24119.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

CGAAACAACACAGCGAGUUAAAAUAAGGCUUAGUCCGUACUCAACUUGAAAAGGUGGCACCGAUUCGGUGUUUUU

Entity 4 Entity 4 polymer

Description description	DNA (43-MER)
Molecular weight formula_weight	15003.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GATGTCTTCCAATTTACTACTCGTTCTGGTGTTTCTCGAGGCGTCAGCC

Entity 5 Entity 5 polymer

Description description	DNA (43-MER)
Molecular weight formula_weight	15182.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

GGCTGACGCCTCGAGAAACACCAGAACGAGTAGTAAATTGGAAGACATC

Entity 6 Entity 6 polymer

Description description	CRISPR-associated endonuclease Cas1
Molecular weight formula_weight	34854.9 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	F,G

MAGWRTVVVNIHSKLSYKNNHLIFRNSYKTEMIHLSEIDILLLETTDIVLTTMLVKRLVDENILVIFCDDKRLPTAFLTPYYARHDSSLQIARQIAWKENVKCEVWTAIIAQKILNQSYYLGECSFFEKSQSIMELYHGLERFDPSNREGHSARIYFNTLFGNDFTRESDNDINAALDYGYTLLLSMFAREVVVCGCMTQIGLKHANQFNQFNLASDIMEPFRPIIDRIVYQNRHNNFVKIKKELFSIFSETYLYNGKEMYLSNIVSDYTKKVIKALNQLGEEIPEFRMSGHHHHHH

Source Source

Source organism organism	Streptococcus thermophilus DGCC 7710
NCBI taxonomy ID ncbi_taxonomy_id	1268061
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MSYRYMRMILMFDMPTDTAEERKAYRKFRKFLLSEGFIMHQFSVYSKLLLNHTANTAMVGRLKANNPKKGNITILTVTEKQFARMIYLYGDKNTSIANSEERLVFLGDNYCDED

Source Source

Source organism organism	Streptococcus thermophilus DGCC 7710
NCBI taxonomy ID ncbi_taxonomy_id	1268061
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 8 Entity 8 polymer

Description description	CRISPR-associated protein Csn2
Molecular weight formula_weight	27459.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,L,N,M

MGHHHHHHENLYFQGGMKINFSLLDEPMEVNLGTVLVIEDVSVFAQLVKEFYQYDEQSNLTIFDSKIRSIRSSELLLITDILGYDINTSQVLKLLHTDIVSQLNDKPEVRSEIDSLVSLITDIIMAECIENELDIEYDEITLLELIKALGVRIETKSCTVFEKIFEILQIFKYLVKKRILVFVNSLSYFSKDEIYQILEYTKLSQADVLFLEPRQIEGIQQFILDKDYILMPYNN

Source Source

Source organism organism	Streptococcus thermophilus DGCC 7710
NCBI taxonomy ID ncbi_taxonomy_id	1268061
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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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	triclinic

Resolution resolution	3.62 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	24394

PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system

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

CRISPR-associated endonuclease Cas9

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9q85__assembly_1__model_1

9q85__assembly_1__model_1 | I(q)

9q85__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 non-polymer

7. Citations (1)