5J0N: Lambda excision HJ intermediate

Lambda excision HJ intermediate. Determined by electron microscopy at 11.0 Å resolution. Released 8 Feb 2017.

Method: Electron microscopy
Resolution: 11.0 Å
Organisms: Enterobacteria phage lambda, Escherichia coli
Chains: 15
Atoms: 24,762
Mol. weight: 372.05 kDa
Released: 8 Feb 2017

Explore 5J0N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J0N contains 91 α-helices and 100 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain E: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	76-88	13
α-helix	94-108	15
α-helix	116-118	3
α-helix	121-133	13
α-helix	137-157	21
α-helix	170-172	3
β-strand	177	1	1
α-helix	182-191	10
α-helix	199-208	10
α-helix	213-216	4
β-strand	220	1	2
β-strand	230-232	3	3
β-strand	239-241	3	3
β-strand	247-248	2	4
β-strand	253-254	2	4
α-helix	255-264	10
β-strand	270	1	2
β-strand	273	1	5
β-strand	279	1	5
α-helix	282-285	4
α-helix	287-296	10
β-strand	303	1	1
α-helix	309-318	10
α-helix	324-331	8
β-strand	350	1	6

Chain F: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	17-18	2	7
β-strand	24-27	4	7
β-strand	34-36	3	7
α-helix	41-44	4
α-helix	51-53	3
α-helix	79-87	9
α-helix	96-108	13
α-helix	112	1
α-helix	121-132	12
α-helix	137-155	19
α-helix	164-166	3
β-strand	177	1	8
α-helix	183-190	8
α-helix	191-193	3
α-helix	197-208	12
α-helix	213-216	4
β-strand	220	1	9
β-strand	224-225	2	10
β-strand	228-232	5	10
β-strand	239-243	5	10
β-strand	247-248	2	11
β-strand	253-254	2	11
α-helix	255-261	7
α-helix	262-266	5
β-strand	270	1	9
β-strand	273	1	12
β-strand	279	1	12
α-helix	280-281	2
α-helix	282-296	15
β-strand	303	1	8
α-helix	309-321	13
α-helix	326-329	4
β-strand	351-352	2	3

Chain G: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26	1
β-strand	27	1	13
α-helix	28	1
β-strand	34	1	13
α-helix	41-44	4
α-helix	46-52	7
β-strand	75	1	14
α-helix	76-88	13
α-helix	94-108	15
β-strand	115	1	14
α-helix	121-132	12
α-helix	139-157	19
α-helix	164-166	3
β-strand	177	1	15
α-helix	178-180	3
α-helix	183-191	9
α-helix	197-205	9
α-helix	213-216	4
β-strand	220	1	16
α-helix	221-223	3
β-strand	230-232	3	17
β-strand	239-241	3	17
β-strand	247-248	2	18
β-strand	253-254	2	18
α-helix	255-261	7
α-helix	262-266	5
β-strand	270	1	16
β-strand	273	1	19
β-strand	279	1	19
α-helix	282-285	4
α-helix	287-296	10
β-strand	303	1	15
α-helix	304-305	2
α-helix	309-321	13
α-helix	324-327	4
β-strand	351-352	2	10

Chain H: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	16	1	20
β-strand	25-27	3	20
β-strand	34-36	3	20
α-helix	41-51	11
α-helix	76-87	12
α-helix	95-107	13
α-helix	122-128	7
α-helix	129-131	3
α-helix	137-156	20
α-helix	169-172	4
β-strand	177	1	21
α-helix	182-191	10
α-helix	198-208	11
β-strand	220	1	22
α-helix	221-223	3
β-strand	224-225	2	6
β-strand	228-232	5	6
β-strand	239-243	5	6
β-strand	247-248	2	23
β-strand	253-254	2	23
α-helix	255-259	5
α-helix	261-264	4
β-strand	270	1	22
β-strand	273	1	24
β-strand	279	1	24
α-helix	282-285	4
α-helix	287-295	9
β-strand	303	1	21
α-helix	309-317	9
β-strand	351-352	2	17

Chain I: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	25
α-helix	5-13	9
α-helix	20-40	21
β-strand	44-46	3	26
β-strand	50-57	8	26
β-strand	60	1	27
β-strand	73	1	27
β-strand	76-83	8	26
α-helix	85-91	7

Chain J: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	26
α-helix	5-13	9
α-helix	19-39	21
α-helix	41-42	2
β-strand	43-45	3	25
β-strand	49-55	7	25
β-strand	61	1	28
β-strand	70	1	28
β-strand	76-80	5	25
α-helix	84-90	7

Chain K: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	29
α-helix	5-16	12
α-helix	20-40	21
β-strand	44-46	3	30
β-strand	50-52	3	30
β-strand	54-57	4	31
β-strand	60	1	32
β-strand	73	1	32
β-strand	76-79	4	31
β-strand	82	1	30
α-helix	85-89	5

Chain L: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	30
α-helix	3-13	11
α-helix	19-39	21
β-strand	43-45	3	29
β-strand	49-56	8	29
β-strand	61	1	33
β-strand	70	1	33
β-strand	75-80	6	29
α-helix	84-90	7

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
attP(-117 to +79)	A	DNA	197	Enterobacteria phage lambda
attB(-21) to attP(+117)	B	DNA	139	Enterobacteria phage lambda
attB(-19 to +21)	C	DNA	41	Escherichia coli
attP(-79) to attB(+19)	D	DNA	99	Enterobacteria phage lambda
Integrase	E, F, G, H	protein	356	Enterobacteria phage lambda	P03700
Integration host factor subunit alpha	I, K	protein	96	Escherichia coli	P0A6X7 (AlphaFold model)
Integration host factor subunit beta	J, L	protein	94	Escherichia coli	P0A6Y1 (AlphaFold model)
Excisionase	M, N, O	protein	55	Enterobacteria phage lambda	P03699

Sequence of entity 1 (A), FASTA

>5J0N_1 attP(-117 to +79) (chains A)
GTCGGCATAGTGACTGCATATGTTGTGTTTTACAGTATTATGTAGTCTGTTTTTTATGCA
AAATCTAATTTAATATATTGATATTTATATCATTTTACGTTTCTCGTTCAGCTTTAATAC
AATAAGTTGGAATTCTAAAAAAGCATTGCTTATCAATTTGTTGCAACGAACAGGTCACTA
TCAGTCAAAATATTGAT

Sequence of entity 2 (B), FASTA

>5J0N_2 attB(-21) to attP(+117) (chains B)
CCGTTTCGCTCAAGTTAGTATATTAAAGCTGAACGAGAAACGTAAAATGATATAAATATC
AATATATTAAATTAGATTTTGCATAAAAAACAGACTACATAATACTGTAAAACACAACAT
ATGCAGTCACTATGCCGAC

Sequence of entity 3 (C), FASTA

>5J0N_3 attB(-19 to +21) (chains C)
CCGTTGAAGCCTGCTTTTTTATACTAACTTGAGCGAAACGG

Sequence of entity 4 (D), FASTA

>5J0N_4 attP(-79) to attB(+19) (chains D)
ATCAATATTTTGACTGATAGTGACCTGTTCGTTGCAACAAATTGATAAGCAATGCTTTTT
TAGAATTCCAACTTATTGTAAAAAAGCAGGCTTCAACGG

Sequence of entity 5 (E, F, G, H), FASTA

>5J0N_5 Integrase (chains E, F, G, H)
MGRRRSHERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHK
HKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDIT
TKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRL
TADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKI
AIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSF
EGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK

Sequence of entity 6 (I, K), FASTA

>5J0N_6 Integration host factor subunit alpha (chains I, K)
ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP
GRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK

Sequence of entity 7 (J, L), FASTA

>5J0N_7 Integration host factor subunit beta (chains J, L)
MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRT
GRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG

Sequence of entity 8 (M, N, O), FASTA

>5J0N_8 Excisionase (chains M, N, O)
MYLTLQEWNARQRRPRSLETVRRWVRESRIFPPPVKDGREYLFHESAVKVDLNRP

Primary citation

Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction. Laxmikanthan, G., Xu, C., Brilot, A.F. et al. Elife (2016) 5. DOI 10.7554/eLife.14313 · PubMed

Other PDB entries of the same protein (UniProt P03700), best resolution first:

1AE9 1.9 Å, Structure of the lambda integrase catalytic core
2OXO 2.0 Å, Crystallization and structure determination of the core-binding domain of bacteriophage…
1Z19 2.8 Å, Crystal structure of a lambda integrase(75-356) dimer bound to a COC' core site
1P7D 2.95 Å, Crystal structure of the Lambda Integrase (residues 75-356) bound to DNA
1Z1B 3.8 Å, Crystal structure of a lambda integrase dimer bound to a COC' core site
1Z1G 4.4 Å, Crystal structure of a lambda integrase tetramer bound to a Holliday junction
1KJK Solution structure of the lambda integrase amino-terminal domain
2WCC phage lambda IntDBD1-64 complex with p prime 2 DNA

Browse structure collections

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