5j0n

Lambda excision HJ intermediate

Method: ELECTRON MICROSCOPY

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

Integrase

Enterobacteria phage lambda

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 4	attP(-117 to +79) × 1 attB(-21) to attP(+117) × 1 attB(-19 to +21) × 1 attP(-79) to attB(+19) × 1 Integration host factor subunit alpha × 2 （B7MAS3） Integration host factor subunit beta × 2 （B7MHM1） Excisionase × 3 （P03699）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VINT_LAMBD
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–356； UniProt 1–356 Author chain F； PDBConstruct 1–356； UniProt 1–356 Author chain G； PDBConstruct 1–356； UniProt 1–356 Author chain H； PDBConstruct 1–356； UniProt 1–356

Integration host factor subunit alpha

Escherichia coli

UniProt B7MAS3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 4	attP(-117 to +79) × 1 attB(-21) to attP(+117) × 1 attB(-19 to +21) × 1 attP(-79) to attB(+19) × 1 Integrase × 4 （P03700） Integration host factor subunit beta × 2 （B7MHM1） Excisionase × 3 （P03699）	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	6
Chains and sequence ranges	Author chain I； PDBConstruct 1–96； UniProt 2–97 Author chain K； PDBConstruct 1–96； UniProt 2–97

Integration host factor subunit beta

Escherichia coli

UniProt B7MHM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 4	attP(-117 to +79) × 1 attB(-21) to attP(+117) × 1 attB(-19 to +21) × 1 attP(-79) to attB(+19) × 1 Integrase × 4 （P03700） Integration host factor subunit alpha × 2 （B7MAS3） Excisionase × 3 （P03699）	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	7
Chains and sequence ranges	Author chain J； PDBConstruct 1–94； UniProt 1–94 Author chain L； PDBConstruct 1–94； UniProt 1–94

Excisionase

Enterobacteria phage lambda

UniProt P03699

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 4	attP(-117 to +79) × 1 attB(-21) to attP(+117) × 1 attB(-19 to +21) × 1 attP(-79) to attB(+19) × 1 Integrase × 4 （P03700） Integration host factor subunit alpha × 2 （B7MAS3） Integration host factor subunit beta × 2 （B7MHM1）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VXIS_LAMBD
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain M； PDBConstruct 1–55； UniProt 1–55 Author chain N； PDBConstruct 1–55； UniProt 1–55 Author chain O； PDBConstruct 1–55； UniProt 1–55

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	5j0n
Deposition date deposition_date	2016-03-28
Structure title title	Lambda excision HJ intermediate
Keywords keywords	bacteriophage lambda, excision, site-specific recombination, Holliday junction, TRANSFERASE, HYDROLASE-DNA complex; TRANSFERASE, HYDROLASE/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.

5j0n__assembly_1__model_1

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

Download this curve (.dat)

5j0n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j0n__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)	60.61 Å
Total Rg	60.85 Å
Atom count	29353
Residues	2349
Excluded volume	409490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j0n__assembly_1__model_1`	pentadecameric （15）	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	attP(-117 to +79)
Molecular weight formula_weight	60791.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	29353

GTCGGCATAGTGACTGCATATGTTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCAAAATCTAATTTAATATATTGATATTTATATCATTTTACGTTTCTCGTTCAGCTTTAATACAATAAGTTGGAATTCTAAAAAAGCATTGCTTATCAATTTGTTGCAACGAACAGGTCACTATCAGTCAAAATATTGAT

Entity 2 Entity 2 polymer

Description description	attB(-21) to attP(+117)
Molecular weight formula_weight	42883.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CCGTTTCGCTCAAGTTAGTATATTAAAGCTGAACGAGAAACGTAAAATGATATAAATATCAATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACATATGCAGTCACTATGCCGAC

Entity 3 Entity 3 polymer

Description description	attB(-19 to +21)
Molecular weight formula_weight	12607.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CCGTTGAAGCCTGCTTTTTTATACTAACTTGAGCGAAACGG

Entity 4 Entity 4 polymer

Description description	attP(-79) to attB(+19)
Molecular weight formula_weight	30552.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

ATCAATATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATTGATAAGCAATGCTTTTTTAGAATTCCAACTTATTGTAAAAAAGCAGGCTTCAACGG

Entity 5 Entity 5 polymer

Description description	Integrase
Molecular weight formula_weight	40373.2 kDa
EC 编号 ec_number	2.7.7.-, 3.1.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MGRRRSHERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK

Source Source

Source organism organism	Enterobacteria phage lambda
NCBI taxonomy ID ncbi_taxonomy_id	10710
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Integration host factor subunit alpha
Molecular weight formula_weight	10998.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K

ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Integration host factor subunit beta
Molecular weight formula_weight	10671.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,L

MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Excisionase
Molecular weight formula_weight	6793.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MYLTLQEWNARQRRPRSLETVRRWVRESRIFPPPVKDGREYLFHESAVKVDLNRP

Source Source

Source organism organism	Enterobacteria phage lambda
NCBI taxonomy ID ncbi_taxonomy_id	10710
Host organism host_organism	Escherichia coli

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Resolution resolution	11.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	10956

Lambda excision HJ intermediate

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

Integrase

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

Excisionase

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

5j0n__assembly_1__model_1

5j0n__assembly_1__model_1 | I(q)

5j0n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

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

Source Source

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

7. Citations (1)