5IKN: T7 Replisome in the Absence of DNA

Crystal Structure of the T7 Replisome in the Absence of DNA. Determined by X-ray diffraction at 4.8 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 4.8 Å
Organisms: Enterobacteria phage T7, Escherichia coli O157:H7
Chains: 13
Atoms: 43,846
Mol. weight: 650.06 kDa
Released: 7 Dec 2016

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

Secondary structure: helices and β-sheets

5IKN contains 268 α-helices and 276 β-strands across 13 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 A: 32 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	18-25	8	1
β-strand	30	1	1
β-strand	33-34	2	1
α-helix	39-52	14
β-strand	56-58	3	1
α-helix	61-65	5
α-helix	66-75	10
α-helix	85-87	3
β-strand	88-90	3	1
α-helix	91-98	8
α-helix	106-112	7
α-helix	125-132	8
α-helix	141-149	9
α-helix	165-186	22
α-helix	198-200	3
α-helix	203-209	7
α-helix	212-230	19
β-strand	232-233	2	2
β-strand	234	1	3
α-helix	236-256	21
α-helix	342-346	5
β-strand	356	1	4
α-helix	361	1
β-strand	362	1	4
α-helix	363	1
α-helix	366-371	6
α-helix	377-399	23
α-helix	406-409	4
β-strand	410	1	2
β-strand	415-416	2	2
β-strand	419-421	3	5
β-strand	431-433	3	5
α-helix	448-454	7
β-strand	455	1	3
β-strand	456	1	6
α-helix	457-459	3
β-strand	461	1	7
α-helix	467	1
β-strand	468	1	7
α-helix	469	1
β-strand	470-476	7	8
α-helix	479-492	14
α-helix	495-502	8
α-helix	505-513	9
α-helix	518-529	12
α-helix	534-538	5
α-helix	545-558	14
α-helix	560-570	11
β-strand	593-594	2	9
β-strand	600-601	2	9
α-helix	610-636	27
β-strand	640	1	8
β-strand	646-652	7	8
β-strand	655-660	6	8
α-helix	663-683	21
β-strand	692-697	6	8
β-strand	699	1	6

Chain B: 33 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	10
β-strand	18-25	8	10
β-strand	30-34	5	10
α-helix	36-38	3
α-helix	39-51	13
β-strand	56-58	3	10
α-helix	61-65	5
α-helix	66-75	10
α-helix	85-87	3
β-strand	89-90	2	10
α-helix	91-98	8
α-helix	102-112	11
α-helix	125-132	8
α-helix	139-148	10
α-helix	165-186	22
α-helix	198-200	3
α-helix	203-209	7
α-helix	212-230	19
β-strand	232-233	2	11
β-strand	234	1	12
α-helix	236-259	24
α-helix	339-342	4
α-helix	366-371	6
α-helix	377-399	23
α-helix	406-409	4
β-strand	410	1	11
β-strand	415-416	2	11
β-strand	419-421	3	13
β-strand	431-433	3	13
α-helix	437-439	3
α-helix	440-442	3
α-helix	448-454	7
β-strand	455	1	12
α-helix	457-459	3
β-strand	470-476	7	14
α-helix	479-492	14
α-helix	495-502	8
α-helix	505-513	9
α-helix	518-530	13
α-helix	535-538	4
α-helix	549-558	10
α-helix	560-568	9
β-strand	574-576	3	15
β-strand	579-580	2	16
β-strand	583-584	2	16
β-strand	587-588	2	15
β-strand	593-594	2	17
β-strand	600-601	2	17
α-helix	610-636	27
α-helix	638-639	2
β-strand	640	1	14
β-strand	646-652	7	14
β-strand	655-660	6	14
α-helix	663-683	21
α-helix	689-690	2
β-strand	692-697	6	14

Chain C: 33 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	18
β-strand	18-25	8	18
β-strand	30-34	5	18
α-helix	36-38	3
α-helix	39-52	14
β-strand	56-58	3	18
α-helix	61-65	5
α-helix	66-75	10
α-helix	85-87	3
β-strand	88-90	3	18
α-helix	91-98	8
α-helix	103-112	10
α-helix	117-119	3
α-helix	125-132	8
α-helix	139-148	10
α-helix	165-186	22
α-helix	203-209	7
α-helix	212-230	19
β-strand	232-233	2	19
β-strand	234	1	20
α-helix	236-259	24
α-helix	339-346	8
β-strand	356	1	21
α-helix	361	1
β-strand	362	1	21
α-helix	363	1
α-helix	366-371	6
α-helix	377-399	23
β-strand	410	1	19
β-strand	415-416	2	19
β-strand	419-421	3	22
β-strand	431-433	3	22
α-helix	440-442	3
α-helix	448-453	6
β-strand	455	1	20
β-strand	456	1	23
α-helix	457-459	3
β-strand	470-476	7	24
α-helix	479-492	14
α-helix	495-502	8
α-helix	505-513	9
α-helix	518-529	12
α-helix	534-538	5
α-helix	539-541	3
α-helix	545-558	14
α-helix	560-570	11
β-strand	579-580	2	25
β-strand	583-584	2	25
β-strand	593-594	2	26
β-strand	600-601	2	26
α-helix	610-635	26
α-helix	638-639	2
β-strand	640	1	24
β-strand	646-652	7	24
β-strand	655-660	6	24
α-helix	663-683	21
β-strand	692-697	6	24
β-strand	699	1	23

Chain D: 21 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66	1	27
α-helix	67-69	3
β-strand	77	1	27
β-strand	81	1	28
β-strand	86	1	28
α-helix	88-94	7
β-strand	96-99	4	27
β-strand	106-112	7	27
β-strand	118-124	7	27
β-strand	130-134	5	27
β-strand	141-142	2	29
α-helix	144-146	3
β-strand	152-156	5	30
α-helix	159-168	10
β-strand	175-176	2	30
β-strand	177-178	2	29
α-helix	185-191	7
α-helix	193-196	4
β-strand	201-205	5	30
α-helix	210-220	11
β-strand	228-230	3	30
α-helix	238-242	5
α-helix	252-256	5
β-strand	258	1	30
α-helix	272-281	10
α-helix	295-299	5
β-strand	307-311	5	31
α-helix	318-331	14
β-strand	337-341	5	31
α-helix	346-357	12
α-helix	366-375	10
α-helix	377-386	10
β-strand	391-392	2	31
α-helix	402-404	3
α-helix	406-411	6
α-helix	412-416	5
β-strand	420-424	5	31
α-helix	439-456	18
β-strand	459-463	5	31
β-strand	466	1	32
β-strand	477	1	33
β-strand	486	1	32
α-helix	492-495	4
β-strand	498-503	6	31
β-strand	505	1	33
β-strand	513-521	9	31
β-strand	528-536	9	31
β-strand	541-545	5	31

Chain E: 23 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	34
α-helix	67-70	4
β-strand	77	1	34
β-strand	81	1	35
β-strand	86	1	35
α-helix	88-94	7
β-strand	96-101	6	34
β-strand	104-112	9	34
β-strand	118-124	7	34
β-strand	130-134	5	34
β-strand	141-142	2	36
α-helix	144-146	3
β-strand	150-156	7	37
α-helix	159-168	10
β-strand	175-176	2	37
β-strand	177-178	2	36
α-helix	185-191	7
α-helix	193-196	4
β-strand	199-205	7	37
α-helix	210-220	11
β-strand	230	1	37
α-helix	238-242	5
α-helix	251-254	4
α-helix	269-271	3
α-helix	272-281	10
α-helix	295-299	5
β-strand	307-312	6	38
α-helix	318-331	14
β-strand	337-341	5	38
α-helix	346-357	12
α-helix	366-374	9
α-helix	377-386	10
β-strand	391-392	2	38
α-helix	402-404	3
α-helix	406-410	5
α-helix	411-416	6
β-strand	420-424	5	38
α-helix	439-456	18
β-strand	459-463	5	38
β-strand	466	1	39
α-helix	475-477	3
β-strand	486	1	39
α-helix	492-495	4
β-strand	498-503	6	38
β-strand	513-521	9	38
β-strand	528-536	9	38
β-strand	541-545	5	38
α-helix	546	1

Chain F: 23 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66	1	40
α-helix	67-70	4
β-strand	77	1	40
β-strand	81	1	41
β-strand	86	1	41
α-helix	88-94	7
β-strand	96-99	4	40
β-strand	106-112	7	40
β-strand	118-124	7	40
β-strand	130-134	5	40
β-strand	141-142	2	42
α-helix	144-146	3
β-strand	150-156	7	43
α-helix	159-162	4
α-helix	165-168	4
β-strand	175-176	2	43
β-strand	177-178	2	42
α-helix	185-191	7
α-helix	193-196	4
β-strand	199-205	7	43
α-helix	210-217	8
α-helix	219-222	4
β-strand	228-230	3	43
α-helix	238-242	5
α-helix	248-254	7
α-helix	272-281	10
α-helix	295-299	5
β-strand	307-311	5	44
α-helix	319-331	13
β-strand	337-341	5	44
α-helix	346-357	12
α-helix	362-364	3
α-helix	366-374	9
α-helix	377-386	10
β-strand	391-393	3	44
α-helix	406-411	6
β-strand	420-424	5	44
α-helix	439-456	18
β-strand	459-464	6	44
β-strand	466	1	45
β-strand	477	1	46
β-strand	486	1	45
α-helix	492-495	4
β-strand	498-503	6	44
β-strand	505	1	46
β-strand	513-521	9	44
β-strand	528-535	8	44
β-strand	542-544	3	44
α-helix	545	1

Chain G: 22 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	47
α-helix	68-70	3
α-helix	71-73	3
β-strand	77	1	47
β-strand	81	1	48
β-strand	86	1	48
α-helix	88-94	7
β-strand	96-99	4	47
β-strand	106-112	7	47
β-strand	118-124	7	47
β-strand	130-134	5	47
β-strand	141-142	2	49
α-helix	144-146	3
β-strand	152-156	5	50
α-helix	159-168	10
β-strand	175-176	2	50
β-strand	177-178	2	49
α-helix	185-191	7
α-helix	193-196	4
β-strand	201-205	5	50
α-helix	210-220	11
β-strand	228-230	3	50
α-helix	238-242	5
α-helix	248-255	8
α-helix	273-281	9
β-strand	287	1	51
α-helix	295-299	5
β-strand	302	1	51
β-strand	307-311	5	52
α-helix	318-331	14
β-strand	337-341	5	52
α-helix	346-357	12
α-helix	366-373	8
α-helix	377-385	9
α-helix	386-388	3
β-strand	391-392	2	52
α-helix	402-404	3
α-helix	406-411	6
α-helix	412-416	5
β-strand	420-424	5	52
α-helix	439-456	18
β-strand	459-463	5	52
β-strand	466	1	53
β-strand	477	1	54
β-strand	486	1	53
α-helix	492-495	4
β-strand	498-503	6	52
β-strand	505	1	54
β-strand	513-521	9	52
β-strand	528-535	8	52
β-strand	542-545	4	52

Chain H: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	65	1
β-strand	66	1	55
α-helix	67-70	4
β-strand	77	1	55
β-strand	81	1	56
β-strand	86	1	56
α-helix	88-94	7
β-strand	96-99	4	55
β-strand	106-112	7	55
β-strand	118-124	7	55
β-strand	130-134	5	55
β-strand	141-142	2	57
α-helix	144-146	3
β-strand	150-156	7	58
α-helix	159-168	10
β-strand	175-176	2	58
β-strand	177-178	2	57
α-helix	185-191	7
α-helix	193-196	4
β-strand	199-205	7	58
α-helix	210-221	12
β-strand	228-230	3	58
α-helix	238-242	5
α-helix	248-252	5
α-helix	272-280	9
α-helix	295-299	5
β-strand	307-312	6	59
α-helix	318-331	14
β-strand	337-341	5	59
α-helix	346-357	12
α-helix	366-374	9
α-helix	378-386	9
β-strand	392-393	2	59
α-helix	402-404	3
α-helix	406-411	6
α-helix	412-416	5
β-strand	420-424	5	59
α-helix	439-456	18
β-strand	459-463	5	59
α-helix	492-495	4
β-strand	498-503	6	59
β-strand	513-521	9	59
β-strand	528-535	8	59
β-strand	542-544	3	59

5 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
DNA-directed DNA polymerase	A, B, C	protein	704	Enterobacteria phage T7	P00581
DNA primase/helicase	D, E, F, G, H, I, J	protein	486	Enterobacteria phage T7	P03692
Thioredoxin-1	K, L, M	protein	105	Escherichia coli O157:H7	P0AA27 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>5IKN_1 DNA-directed DNA polymerase (chains A, B, C)
MIVSAIAANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHN
GHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRF
GSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKA
LLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIE
ELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKK
PKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKG
APVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSV
NPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLE
LRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQI
VGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRK
VHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGC
RTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH

Sequence of entity 2 (D, E, F, G, H, I, J), FASTA

>5IKN_2 DNA primase/helicase (chains D, E, F, G, H, I, J)
MTYNVWNFGESNGRYSALTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKV
RDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGAS
AAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANECHL
NGHDREIMEQVWNAGPWIPDGVVSALSLRERIREHLSSEESVGLLFSGCTGINDKTLGAR
GGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLR
QSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIIL
DHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHEEGRPVSI
TDLRGSGALRQLSDTIIALERNQQGDMPNLVLVRILKCRFTGDTGIAGYMEYNKETGWLE
PSSYSG

Sequence of entity 3 (K, L, M), FASTA

>5IKN_3 Thioredoxin-1 (chains K, L, M)
KIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQ
NPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL

Primary citation

Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Wallen, J.R., Zhang, H., Weis, C. et al. Structure (2017) 25:157-166. DOI 10.1016/j.str.2016.11.019 · PubMed

Other PDB entries of the same protein (UniProt P00581), best resolution first:

1X9M 2.1 Å, T7 DNA polymerase in complex with an N-2-acetylaminofluorene-adducted DNA
1SL1 2.2 Å, Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn…
1T7P 2.2 Å, T7 DNA polymerase complexed to DNA primer/template,a nucleoside triphosphate, and its…
1TK5 2.2 Å, T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand
1SKS 2.3 Å, Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn…
1SKW 2.3 Å, Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a…
1SL2 2.3 Å, Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn…
1TK0 2.3 Å, T7 DNA polymerase ternary complex with 8 oxo guanosine and ddCTP at the insertion site
1X9W 2.3 Å, T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2…
1SKR 2.4 Å, T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP
1TKD 2.49 Å, T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site
1TK8 2.5 Å, T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site

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