8flj

Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA

Method: ELECTRON MICROSCOPY

▼

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

CRISPR-associated endonuclease Cas1

Pseudomonas aeruginosa PA14

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 4	Integration host factor subunit alpha × 2 （Q02NN5） Integration host factor subunit beta × 2 （Q02PW7） CRISPR leader, sense strand of DNA × 1 CRISPR leader and repeat, anti-sense strand of DNA × 1 CRISPR repeat and prespacer, sense strand of DNA × 1 Prespacer, anti-sense strand of DNA × 1 CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST × 2 （Q02ML8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS1_PSEAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–341； UniProt 1–324 Author chain B； PDBConstruct 18–341； UniProt 1–324 Author chain C； PDBConstruct 18–341； UniProt 1–324 Author chain D； PDBConstruct 18–341； UniProt 1–324

Integration host factor subunit alpha

Pseudomonas aeruginosa PA14

UniProt Q02NN5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 4	CRISPR-associated endonuclease Cas1 × 4 （Q02ML7） Integration host factor subunit beta × 2 （Q02PW7） CRISPR leader, sense strand of DNA × 1 CRISPR leader and repeat, anti-sense strand of DNA × 1 CRISPR repeat and prespacer, sense strand of DNA × 1 Prespacer, anti-sense strand of DNA × 1 CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST × 2 （Q02ML8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IHFA_PSEAB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 3–102； UniProt 1–100 Author chain G； PDBConstruct 3–102； UniProt 1–100

Integration host factor subunit beta

Pseudomonas aeruginosa PA14

UniProt Q02PW7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 4	CRISPR-associated endonuclease Cas1 × 4 （Q02ML7） Integration host factor subunit alpha × 2 （Q02NN5） CRISPR leader, sense strand of DNA × 1 CRISPR leader and repeat, anti-sense strand of DNA × 1 CRISPR repeat and prespacer, sense strand of DNA × 1 Prespacer, anti-sense strand of DNA × 1 CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST × 2 （Q02ML8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IHFB_PSEAB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 3–96； UniProt 1–94 Author chain H； PDBConstruct 3–96； UniProt 1–94

CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST

Pseudomonas aeruginosa PA14

UniProt Q02ML8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 4	CRISPR-associated endonuclease Cas1 × 4 （Q02ML7） Integration host factor subunit alpha × 2 （Q02NN5） Integration host factor subunit beta × 2 （Q02PW7） CRISPR leader, sense strand of DNA × 1 CRISPR leader and repeat, anti-sense strand of DNA × 1 CRISPR repeat and prespacer, sense strand of DNA × 1 Prespacer, anti-sense strand of DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS3_PSEAB
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain M； PDBConstruct 1–1076； UniProt 1–1076 Author chain N； PDBConstruct 1–1076； UniProt 1–1076

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8flj
Deposition date deposition_date	2022-12-21
Structure title title	Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA
Keywords keywords	;DNA integration, maintenance of CRISPR repeat elements, IHF-DNA complex, Enzymes altering nucleic acid conformation, Site specific endodeoxyribonucleases: cleavage is not sequence specific, Nucleotidyltransferases, GO:0008301, RECOMBINATION, DNA BINDING PROTEIN, HYDROLASE-DNA complex ;; RECOMBINATION, DNA BINDING PROTEIN, HYDROLASE/DNA
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8flj__assembly_1__model_1

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

Download this curve (.dat)

8flj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8flj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	62.48 Å
Rg (electron density)	61.37 Å
Total Rg	61.22 Å
Atom count	57091
Residues	3899
Excluded volume	530970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8flj__assembly_1__model_1`	tetradecameric （14）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated endonuclease Cas1
Molecular weight formula_weight	38267.1 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	A,B,C,D
Atom count atom_count	57091

MWSHPQFEKENLYFQGSMDDISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNLSRAQALDFMIDTLKDVAQRSTVSA

Source Source

Source organism organism	Pseudomonas aeruginosa PA14
NCBI taxonomy ID ncbi_taxonomy_id	652611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Integration host factor subunit alpha
Molecular weight formula_weight	11646.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G

GPMGALTKAEIAERLYEELGLNKREAKELVELFFEEIRQALEHNEQVKLSGFGNFDLRDKRQRPGRNPKTGEEIPITARRVVTFRPGQKLKARVEAYAGTKS

Source Source

Source organism organism	Pseudomonas aeruginosa PA14
NCBI taxonomy ID ncbi_taxonomy_id	652611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Integration host factor subunit beta
Molecular weight formula_weight	10805.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H

GPMTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFKPGKELRDRVNEPE

Source Source

Source organism organism	Pseudomonas aeruginosa PA14
NCBI taxonomy ID ncbi_taxonomy_id	652611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	CRISPR leader, sense strand of DNA
Molecular weight formula_weight	42935.6 kDa
Mutation mutation	C30A,T31A,T32A,C34A,G35A,G97A,G98A,T99A,T101A,T102A,T103C,C104G,T105C,T108C,T109G,C110A,C111A,T112A,A117C,T118G
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

AAGCTTCCGACCCTTTTTTCGGACGATTTAAAAAACCCTTATAAATCAGCAAGTTACGAGACCTCGAAAAAAGAGGGTTTCTGGCGGGAAAAACTCAAAAAACGCTTCGAAATCAACCGGTTATAGGTTTTCGGAGCTA

Entity 5 Entity 5 polymer

Description description	CRISPR leader and repeat, anti-sense strand of DNA
Molecular weight formula_weight	52701.6 kDa
Mutation mutation	A54G,T55G,A60T,G61T,G62T,A63C,A64G,A67G,G68C,A69G,A70T,A71T,A73T,C74T,C75T,C137T,G138T,A140T,A141T,G142T
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TGATTTTCTTAGCTGCCTACACGGCAGTGAACTAGCTCCGAAAACCTATAACCGGTTGATTTCGAAGCGTTTTTTGAGTTTTTCCCGCCAGAAACCCTCTTTTTTCGAGGTCTCGTAACTTGCTGATTTATAAGGGTTTTTTAAATCGTCCGAAAAAAGGGTCGGAAGCTT

Entity 6 Entity 6 polymer

Description description	CRISPR repeat and prespacer, sense strand of DNA
Molecular weight formula_weight	18241.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

GTGCAAGTCGTTTTGCTAGAGCTACATGTTCACTGCCGTGTAGGCAGCTAAGAAAATCA

Entity 7 Entity 7 polymer

Description description	Prespacer, anti-sense strand of DNA
Molecular weight formula_weight	8263.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

GCTCTAGCAAAACGACTTGCACAACGA

Entity 8 Entity 8 polymer

Description description	CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
Molecular weight formula_weight	121273.7 kDa
EC 编号 ec_number	3.1.-.-,3.6.4.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MNILLVSQCEKRALSETRRILDQFAERRGERTWQTPITQAGLDTLRRLLKKSARRNTAVACHWIRGRDHSELLWIVGDASRFNAQGAVPTNRTCRDILRKEDENDWHSAEDIRLLTVMAALFHDIGKASQAFQAKLRNRGKPMADAYRHEWVSLRLFEAFVGPGSSDEDWLRRLADKRETGDAWLSQLARDDRQSAPPGPFQKSRLPPLAQAVGWLIVSHHRLPNGDHRGSASLARLPAPIQSQWCGARDADAKEKAACWQFPHGLPFASAHWRARTALCAQSMLERPGLLARGPALLHDSYVMHVSRLILMLADHHYSSLPADSRLGDPNFPLHANTDRDSGKLKQRLDEHLLGVALHSRKLAGTLPRLERQLPRLARHKGFTRRVEQPRFRWQDKAYDCAMACREQAMEHGFFGLNLASTGCGKTLANGRILYALADPQRGARFSIALGLRSLTLQTGQAYRERLGLGDDDLAILVGGSAARELFEKQQERLERSGSESAQELLAENSHVHFAGTLEDGPLREWLGRNSAGNRLLQAPILACTIDHLMPASESLRGGHQIAPLLRLMTSDLVLDEVDDFDIDDLPALSRLVHWAGLFGSRVLLSSATLPPALVQGLFEAYRSGREIFQRHRGAPGRATEIRCAWFDEFSSQSSAHGAVTSFSEAHATFVAQRLAKLEQLPPRRQAQLCTVHAAGEARPALCRELAGQMNTWMADLHRCHHTEHQGRRISFGLLRLANIEPLIELAQAILAQGAPEGLHVHLCVYHSRHPLLVRSAIERQLDELLKRSDDDAAALFARPTLAKALQASTERDHLFVVLASPVAEVGRDHDYDWAIVEPSSMRSIIQLAGRIRRHRSGFSGEANLYLLSRNIRSLEGQNPAFQRPGFETPDFPLDSHDLHDLLDPALLARIDASPRIVEPFPLFPRSRLVDLEHRRLRALMLADDPPSSLLGVPLWWQTPASLSGALQTSQPFRAGAKERCYALLPDEDDEERLHFSRYEEGTWSNQDNLLRNLDLTYGPRIQTWGTVNYREELVAMAGREDLDLRQCAMRYGEVRLRENTQGWSYHPYLGFKKYN

Source Source

Source organism organism	Pseudomonas aeruginosa PA14
NCBI taxonomy ID ncbi_taxonomy_id	652611
Host organism host_organism	Escherichia coli BL21(DE3)

▶

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	3.480 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.48 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	366794

Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA

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

Integration host factor subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Integration host factor subunit beta

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 nuclease/helicase Cas3 subtype I-F/YPEST

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

8flj__assembly_1__model_1

8flj__assembly_1__model_1 | I(q)

8flj__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 (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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

7. Citations (1)