5wfe

Cas1-Cas2-IHF-DNA holo-complex

Method: ELECTRON MICROSCOPY

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

CRISPR-associated endonuclease Cas1

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 4	CRISPR-associated endoribonuclease Cas2 × 2 （P45956） DNA (28-MER) × 1 DNA (45-MER) × 1 DNA (76-MER) × 1 DNA (61-MER) × 1 Integration host factor subunit alpha × 1 （B7MAS3） Integration host factor subunit beta × 1 （B7MHM1）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 1–305 Author chain B； PDBConstruct 1–305； UniProt 1–305 Author chain C； PDBConstruct 1–305； UniProt 1–305 Author chain D； PDBConstruct 1–305； UniProt 1–305

CRISPR-associated endoribonuclease Cas2

Escherichia coli K-12

UniProt P45956

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 4	CRISPR-associated endonuclease Cas1 × 4 （Q46896） DNA (28-MER) × 1 DNA (45-MER) × 1 DNA (76-MER) × 1 DNA (61-MER) × 1 Integration host factor subunit alpha × 1 （B7MAS3） Integration host factor subunit beta × 1 （B7MHM1）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS2_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–94； UniProt 1–94 Author chain F； PDBConstruct 1–94； UniProt 1–94

Integration host factor subunit alpha

Escherichia coli S88

UniProt B7MAS3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 4	CRISPR-associated endonuclease Cas1 × 4 （Q46896） CRISPR-associated endoribonuclease Cas2 × 2 （P45956） DNA (28-MER) × 1 DNA (45-MER) × 1 DNA (76-MER) × 1 DNA (61-MER) × 1 Integration host factor subunit beta × 1 （B7MHM1）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IHFA_ECO45
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 1–99； UniProt 1–99

Integration host factor subunit beta

Escherichia coli S88

UniProt B7MHM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 4	CRISPR-associated endonuclease Cas1 × 4 （Q46896） CRISPR-associated endoribonuclease Cas2 × 2 （P45956） DNA (28-MER) × 1 DNA (45-MER) × 1 DNA (76-MER) × 1 DNA (61-MER) × 1 Integration host factor subunit alpha × 1 （B7MAS3）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IHFB_ECO45
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–94； UniProt 1–94

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	5wfe
Deposition date deposition_date	2017-07-11
Structure title title	Cas1-Cas2-IHF-DNA holo-complex
Keywords keywords	CRISPR integration complex, DNA, Cas1-Cas2, IHF, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

5wfe__assembly_1__model_1

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

Download this curve (.dat)

5wfe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5wfe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.22 Å
Rg (electron density)	51.68 Å
Total Rg	51.79 Å
Atom count	15523
Residues	1657
Excluded volume	264420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5wfe__assembly_1__model_1`	dodecameric （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 endonuclease Cas1
Molecular weight formula_weight	33235.4 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	15523

MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDAGHRSS

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CRISPR-associated endoribonuclease Cas2
Molecular weight formula_weight	11553.3 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	E,F

MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA (28-MER)
Molecular weight formula_weight	8680.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

AAACACCAGAACGAGTAGTAAATTGGGC

Entity 4 Entity 4 polymer

Description description	DNA (45-MER)
Molecular weight formula_weight	18746.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

ATTTACTACTCGTTCTGGTGTTTCTCGTGTGTTCCCCGCGCCAGCGGGGATAAACCGAGCA

Entity 5 Entity 5 polymer

Description description	DNA (76-MER)
Molecular weight formula_weight	29101.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TGCTCGGTTTATCCCCGCTGGCGCGGGGAACACTCTAAACATAACCTATTATTAATTAATGATTTTTTAAGCCAGTCACAATCTACCAACTTTAT

Entity 6 Entity 6 polymer

Description description	DNA (61-MER)
Molecular weight formula_weight	19286.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATAAAGTTGGTAGATTGTGACTGGCTTAAAAAATCATTAATTAATAATAGGTTATGTTTAGA

Entity 7 Entity 7 polymer

Description description	Integration host factor subunit alpha
Molecular weight formula_weight	11374.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPKDE

Source Source

Source organism organism	Escherichia coli S88
NCBI taxonomy ID ncbi_taxonomy_id	585035
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Integration host factor subunit beta
Molecular weight formula_weight	10671.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG

Source Source

Source organism organism	Escherichia coli S88
NCBI taxonomy ID ncbi_taxonomy_id	585035
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	5wfeA01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5wfeA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

Domain ID domain_id	5wfeB01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5wfeB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

Domain ID domain_id	5wfeC01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5wfeC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

Domain ID domain_id	5wfeD01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5wfeD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

Domain ID domain_id	5wfeK00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	520 — HU Protein; Chain A
Homologous superfamily homologous superfamily	10 — IHF-like DNA-binding proteins

Domain ID domain_id	5wfeL00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	520 — HU Protein; Chain A
Homologous superfamily homologous superfamily	10 — IHF-like DNA-binding proteins

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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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.64 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	86000

Cas1-Cas2-IHF-DNA holo-complex

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5wfe__assembly_1__model_1

5wfe__assembly_1__model_1 | I(q)

5wfe__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

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

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)