9vja

Type I-A CRISPR integrase prespacer catching complex, State II

Method: ELECTRON MICROSCOPY

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

CRISPR-associated endonuclease Cas1

Enterococcus faecalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 2	DNA (51-MER) × 1 DNA (51-MER) × 1 RNA (55-MER) × 1 RNA (83-MER) × 1 Type II-A CRISPR-associated protein Csn2 × 4 （A0A3N3GYE7） CRISPR-associated endonuclease Cas9 × 1 （A0A3N3HFT9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A3N3GDE4_ENTFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain K； PDBConstruct 1–288； UniProt 1–288 Author chain L； PDBConstruct 1–288； UniProt 1–288

Type II-A CRISPR-associated protein Csn2

Enterococcus faecalis

UniProt A0A3N3GYE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 2	CRISPR-associated endonuclease Cas1 × 2 （A0A3N3GDE4） DNA (51-MER) × 1 DNA (51-MER) × 1 RNA (55-MER) × 1 RNA (83-MER) × 1 CRISPR-associated endonuclease Cas9 × 1 （A0A3N3HFT9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A3N3GYE7_ENTFL
Isoform	—
PDB entities	6
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

CRISPR-associated endonuclease Cas9

Enterococcus faecalis

UniProt A0A3N3HFT9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 2	CRISPR-associated endonuclease Cas1 × 2 （A0A3N3GDE4） DNA (51-MER) × 1 DNA (51-MER) × 1 RNA (55-MER) × 1 RNA (83-MER) × 1 Type II-A CRISPR-associated protein Csn2 × 4 （A0A3N3GYE7）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A3N3HFT9_ENTFL
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain S； PDBConstruct 1–1337； UniProt 1–1337

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	9vja
Deposition date deposition_date	2025-06-19
Structure title title	Type I-A CRISPR integrase prespacer catching complex, State II
Keywords keywords	CRISPR, Cas9, Cas1, Csn2 DNA binding protein, DNA BINDING PROTEIN/DNA/RNA, DNA BINDING PROTEIN-DNA-RNA complex; DNA BINDING PROTEIN/DNA/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.

9vja__assembly_1__model_1

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

Download this curve (.dat)

9vja__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vja__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.86 Å
Rg (electron density)	54.53 Å
Total Rg	54.62 Å
Atom count	26425
Residues	2950
Excluded volume	461630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vja__assembly_1__model_1`	11-meric （11）	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 (7)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated endonuclease Cas1
Molecular weight formula_weight	33492.6 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	K,L
Atom count atom_count	26425

MGWRTVVVNKHSKLSYKNNHLVFKAIDHQELIHLSEIDVLLLETTDISLTTMLLKRLIDEKILVLFCDDKRLPIGKILPFYGRHDSSLQLTRQLAWTEERKGQVWTAIIAQKITNQSLHLAQRDYGQKAAALLAMRAELRLFDPANREGHAARSYFNTLFGNDFTREQENDINAGLNYGYTLLLSIFARELVQTGCFTQLGLKHANQFNDFNLASDLMEPFRPLVDQIIYENRKEAFPIMKRKLFALFMNTYMYKKKQMFLTNIATDYTKHVVKVLNQEEEGVPEFGI

Source Source

Source organism organism	Enterococcus faecalis
NCBI taxonomy ID ncbi_taxonomy_id	1351
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (51-MER)
Molecular weight formula_weight	15774.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

AGCGCTCTGAATGCTAGATCACGTTATGAAACAGACATAGCGGTACAAAAA

Entity 3 Entity 3 polymer

Description description	DNA (51-MER)
Molecular weight formula_weight	15644.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TTTTTGTACCGCTATGTCTGTTTCATAACGTGATCTAGCATTCAGAGCGCT

Entity 4 Entity 4 polymer

Description description	RNA (55-MER)
Molecular weight formula_weight	17561.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	g

GCAAUACUUUGUCUGUAUCGUUUUAGAGUCAUGUUGUUUAGAAUGGUACCAAAAC

Entity 5 Entity 5 polymer

Description description	RNA (83-MER)
Molecular weight formula_weight	26614.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	t

CUUUUGGGACUAUUCUAAACAACAUAGCAAGUUAAAAUAAGGUUUUAACCGUAAUCAACUGUAAAGUGGCGCUGUUUCGGCGC

Entity 6 Entity 6 polymer

Description description	Type II-A CRISPR-associated protein Csn2
Molecular weight formula_weight	25433.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MRVNFSLLEEPIEIEKATFLTIKDVQTFAHLVKLIYQYDGENELKLFDAQQKGLKPTELFVVTDILGYDVNSAATLKLIYGDLEAQLNDKPEVKSMIEKLTGTISQLIGYELLEHEMDLEEDGITVQELFKALGIKIETTSDTIFEKVMEITQVHRYLSKKKLLIFINACTYLTEDEVQQVVEYISLNNVDVLFLEQRVVQNRFQYILDENFYLSYEKA

Source Source

Source organism organism	Enterococcus faecalis
NCBI taxonomy ID ncbi_taxonomy_id	1351
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	CRISPR-associated endonuclease Cas9
Molecular weight formula_weight	155565.3 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	S

MKKDYVIGLDIGTNSVGWAVMTEDYQLVKKKMPIYGNTEKKKIKKNFWGVRLFEEGHTAEDRRLKRTARRRISRRRNRLRYLQAFFEEAMTDLDENFFARLQESFLVPEDKKWHRHPIFAKLEDEVAYHETYPTIYHLRKKLADSSEQADLRLIYLALAHIVKYRGHFLIEGKLSTENISVKEQFQQFMIIYNQTFVNGESRLVSAPLPESVLIEEELTEKASRTKKSEKVLQQFPQEKANGLFGQFLKLMVGNKADFKKVFGLEEEAKITYASESYEEDLEGILAKVGDEYSDVFLAAKNVYDAVELSTILADSDKKSHAKLSSSMIVRFTEHQEDLKKFKRFIRENCPDEYDNLFKNEQKDGYAGYIAHAGKVSQLKFYQYVKKIIQDIAGAEYFLEKIAQENFLRKQRTFDNGVIPHQIHLAELQAIIHRQAAYYPFLKENQEKIEQLVTFRIPYYVGPLSKGDASTFAWLKRQSEEPIRPWNLQETVDLDQSATAFIERMTNFDTYLPSEKVLPKHSLLYEKFMVFNELTKISYTDDRGIKANFSGKEKEKIFDYLFKTRRKVKKKDIIQFYRNEYNTEIVTLSGLEEDQFNASFSTYQDLLKCGLTRAELDHPDNAEKLEDIIKILTIFEDRQRIRTQLSTFKGQFSAEVLKKLERKHYTGWGRLSKKLINGIYDKESGKTILGYLIKDDGVSKHYNRNFMQLINDSQLSFKNAIQKAQSSEHEETLSETVNELAGSPAIKKGIYQSLKIVDELVAIMGYAPKRIVVEMARENQTTSTGKRRSIQRLKIVEKAMAEIGSNLLKEQPTTNEQLRDTRLFLYYMQNGKDMYTGDELSLHRLSHYDIDHIIPQSFMKDDSLDNLVLVGSTENRGKSDDVPSKEVVKDMKAYWEKLYAAGLISQRKFQRLTKGEQGGLTLEDKAHFIQRQLVETRQITKNVAGILDQRYNANSKEKKVQIITLKASLTSQFRSIFGLYKVREVNDYHHGQDAYLNCVVATTLLKVYPNLAPEFVYGEYPKFQTFKENKATAKAIIYTNLLRFFTEDEPRFTKDGEILWSNSYLKTIKKELNYHQMNIVKKVEVQKGGFSKESIKPKGPSNKLIPVKNGLDPQKYGGFDSPIVAYTVLFTHEKGKKPLIKQEILGITIMEKTRFEQNPILFLEEKGFLRPRVLMKLPKYTLYEFPEGRRRLLASAKEAQKGNQMVLPEHLLTLLYHAKQCLLPNQSESLAYVEQHQPEFQEILERVVDFAEVHTLAKSKVQQIVKLFEANQTADVKEIAASFIQLMQFNAMGAPSTFKFFQKDIERARYTSIKEIFDATIIYQSTTGLYETRRKVVD

Source Source

Source organism organism	Enterococcus faecalis
NCBI taxonomy ID ncbi_taxonomy_id	1351
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	3.010 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.01 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	80591

Type I-A CRISPR integrase prespacer catching complex, State II

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

CRISPR-associated endonuclease Cas1

State in the Current Structure

Other States of the Same Protein in the Database

Type II-A CRISPR-associated protein Csn2

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated endonuclease Cas9

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

9vja__assembly_1__model_1

9vja__assembly_1__model_1 | I(q)

9vja__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

7. Citations (1)

Type I-A CRISPR integrase prespacer catching complex, State II

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

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

Type II-A 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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9vja__assembly_1__model_1

9vja__assembly_1__model_1 | I(q)

9vja__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

7. Citations (1)