4Q7J: Complex structure of viral RNA polymerase

Complex structure of viral RNA polymerase. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Aug 2014.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Escherichia coli, Enterobacteria phage Qbeta
Chains: 8
Atoms: 21,369
Mol. weight: 342.76 kDa
Released: 27 Aug 2014

Explore 4Q7J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Q7J contains 114 α-helices and 144 β-strands across 8 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: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-28	10
α-helix	33-51	19
β-strand	59-66	8	1
β-strand	69-76	8	1
α-helix	82-84	3
α-helix	86-102	17
α-helix	107-113	7
α-helix	115-125	11
β-strand	130-138	9	1
β-strand	141-147	7	2
β-strand	151-158	8	2
α-helix	162-175	14
β-strand	179	1	3
α-helix	187-202	16
α-helix	208-226	19
β-strand	227	1	3
β-strand	232	1	4
α-helix	233	1
β-strand	240	1	4
α-helix	241-247	7
β-strand	251-259	9	2
α-helix	271-278	8

Chain B: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	11-18	8	5
α-helix	24-38	15
β-strand	67-70	4	5
β-strand	75-80	6	5
α-helix	84-92	9
β-strand	100-106	7	5
α-helix	115-125	11
β-strand	129-135	7	5
α-helix	143-159	17
β-strand	169-172	4	5
α-helix	174-178	5
α-helix	182-197	16
α-helix	200-204	5
α-helix	209-210	2
β-strand	211-213	3	6
β-strand	216-220	5	6
β-strand	224-230	7	6
β-strand	233	1	6
β-strand	237	1	7
β-strand	241-245	5	6
β-strand	251-259	9	6
β-strand	264-265	2	6
β-strand	267	1	7
β-strand	273-279	7	6
α-helix	283-285	3
β-strand	288	1	8
β-strand	290	1	8
β-strand	291-293	3	6
β-strand	299-310	12	9
β-strand	322	1	10
β-strand	329-332	4	9
β-strand	335-342	8	9
α-helix	343-344	2
β-strand	350	1	10
β-strand	355-368	14	9
β-strand	373-378	6	9
β-strand	381-391	11	9

Chain C: 28 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
α-helix	20-22	3
α-helix	28-39	12
α-helix	43-45	3
α-helix	48-53	6
α-helix	62-73	12
α-helix	89-110	22
α-helix	120-138	19
α-helix	144-150	7
α-helix	168-173	6
β-strand	176-178	3	11
α-helix	183-192	10
β-strand	199-202	4	11
β-strand	207-211	5	12
β-strand	219-223	5	12
α-helix	226-242	17
α-helix	254-265	12
β-strand	269-272	4	13
α-helix	277-280	4
β-strand	282	1	14
α-helix	283-289	7
α-helix	292-301	10
β-strand	305-307	3	12
β-strand	313-315	3	12
β-strand	318	1	14
α-helix	327-345	19
β-strand	354-356	3	13
β-strand	359-363	5	13
α-helix	364-366	3
α-helix	367-377	11
β-strand	387	1	13
β-strand	392-395	4	15
β-strand	398-401	4	15
β-strand	404-405	2	15
α-helix	418-432	15
β-strand	433-434	2	16
β-strand	437-438	2	16
α-helix	440-449	10
α-helix	450-452	3
α-helix	455-459	5
β-strand	461-462	2	17
β-strand	471-472	2	17
α-helix	475-477	3
β-strand	482-484	3	18
β-strand	487-499	13	18
α-helix	504-516	13
α-helix	517-519	3
α-helix	541-543	3
α-helix	548-550	3
β-strand	553-566	14	18

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	23-31	9	19
β-strand	36-39	4	19
β-strand	42	1	11
β-strand	46-48	3	19
β-strand	67-71	5	19
α-helix	79-82	4
α-helix	85-101	17
β-strand	107-115	9	20
β-strand	119-124	6	20
β-strand	127-132	6	20
α-helix	143-145	3
β-strand	151-159	9	20
β-strand	166-169	4	20
α-helix	171-175	5

Chain E: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
α-helix	19-28	10
α-helix	33-51	19
β-strand	59-66	8	21
β-strand	69-76	8	21
α-helix	80-83	4
α-helix	86-101	16
α-helix	107-113	7
α-helix	115-125	11
β-strand	130-138	9	21
β-strand	141-147	7	22
β-strand	151-158	8	22
α-helix	162-175	14
β-strand	179	1	23
α-helix	182-184	3
α-helix	187-202	16
α-helix	208-225	18
β-strand	227	1	23
β-strand	232	1	24
β-strand	240	1	24
α-helix	241-247	7
β-strand	251-259	9	22
α-helix	267-269	3
α-helix	271-278	8
α-helix	279-281	3

Chain F: 13 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
β-strand	11-18	8	25
α-helix	20-22	3
α-helix	24-38	15
β-strand	67-71	5	25
β-strand	74-80	7	25
α-helix	84-92	9
β-strand	100-106	7	25
α-helix	113-125	13
β-strand	130-135	6	25
α-helix	137-139	3
α-helix	143-159	17
β-strand	169-172	4	25
α-helix	174-178	5
α-helix	182-197	16
α-helix	201-204	4
α-helix	209-210	2
β-strand	211-213	3	26
β-strand	216-220	5	26
β-strand	224-230	7	26
β-strand	233	1	26
β-strand	235-237	3	27
β-strand	241-245	5	26
β-strand	251-259	9	26
β-strand	264-265	2	26
β-strand	267-269	3	27
β-strand	273-279	7	26
α-helix	283-285	3
β-strand	288	1	28
β-strand	290	1	28
β-strand	291-293	3	26
β-strand	299-310	12	29
β-strand	322	1	30
β-strand	329-332	4	29
β-strand	335-342	8	29
α-helix	343-344	2
β-strand	350	1	30
β-strand	355-368	14	29
β-strand	373-378	6	29
β-strand	381-391	11	29

Chain G: 28 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
α-helix	28-40	13
α-helix	42-45	4
α-helix	48-53	6
α-helix	62-74	13
α-helix	89-110	22
α-helix	120-138	19
α-helix	144-150	7
β-strand	158	1	31
β-strand	161	1	31
α-helix	168-173	6
β-strand	176	1	32
α-helix	183-191	9
β-strand	199	1	32
β-strand	207-212	6	33
β-strand	218-223	6	33
α-helix	226-242	17
α-helix	243-246	4
α-helix	254-263	10
β-strand	269-273	5	34
α-helix	277-279	3
β-strand	282	1	35
α-helix	283-289	7
α-helix	292-301	10
β-strand	305-307	3	33
β-strand	313-315	3	33
β-strand	318	1	35
α-helix	327-345	19
α-helix	350-352	3
β-strand	354-356	3	34
β-strand	359-363	5	34
α-helix	364-366	3
α-helix	367-377	11
β-strand	387	1	34
β-strand	392-395	4	36
β-strand	398-401	4	36
β-strand	404-405	2	36
α-helix	418-432	15
β-strand	434	1	37
β-strand	437	1	37
α-helix	440-449	10
α-helix	450-452	3
α-helix	455-458	4
β-strand	461-462	2	38
β-strand	471-472	2	38
α-helix	475-477	3
β-strand	482-483	2	39
β-strand	488-500	13	39
α-helix	504-518	15
α-helix	542-544	3
α-helix	548-550	3
β-strand	552-565	14	39

Chain H: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
β-strand	23-24	2	40
β-strand	27-31	5	41
β-strand	36-39	4	41
β-strand	42	1	32
β-strand	46-48	3	41
β-strand	67	1	41
β-strand	70-71	2	40
α-helix	88-103	16
β-strand	108-110	3	42
β-strand	111-115	5	43
β-strand	119-123	5	43
β-strand	128-132	5	43
β-strand	152-154	3	42
β-strand	155-159	5	44
β-strand	166-169	4	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Ts	A, E	protein	282	Escherichia coli	P0A6P1 (AlphaFold model)
Elongation factor Tu 1	B, F	protein	393	Escherichia coli	P0CE47 (AlphaFold model)
Q beta replicase	C, G	protein	594	Enterobacteria phage Qbeta	P14647
30S ribosomal protein S1	D, H	protein	281	Escherichia coli	P0AG67 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>4Q7J_1 Elongation factor Ts (chains A, E)
AEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADGV
IKTKIDGNYGIILEVNCQTDFVAKDAGFQAFADKVLDAAVAGKITDVEVLKAQFEEERVA
LVAKIGENINIRRVAALEGDVLGSYQHGARIGVLVAAKGADEELVKHIAMHVAASKPEFI
KPEDVSAEVVEKEYQVQLDIAMQSGKPKEIAEKMVEGRMKKFTGEVSLTGQPFVMEPSKT
VGQLLKEHNAEVTGFIRFEVGEGIEKVETDFAAEVAAMSKQS

Sequence of entity 2 (B, F), FASTA

>4Q7J_2 Elongation factor Tu 1 (chains B, F)
SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGI
TINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHIL
LGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEG
DAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGE
EVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKP
HTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVV
TLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Sequence of entity 3 (C, G), FASTA

>4Q7J_3 Q beta replicase (chains C, G)
SKTASSRNSLSAQLRRAANTRIEVEGNLALSIANDLLLAYGQSPFNSEAECISFSPRFDG
TPDDFRINYLKAEIMSKYDDFSLGIDTEAVAWEKFLAAEAECALTNARLYRPDYSEDFNF
SLGESCIHMARRKIAKLIGDVPSVEGMLRHCRFSGGATTTNNRSYGHPSFKFALPQACTP
RALKYVLALRASTHFDIRISDISPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGILR
DRLRCWGIDLNDQTINQRRAHEGSVTNNLATVDLSAASDSISLALCELLLPPGWFEVLMD
LRSPKGRLPDGSVVTYEKISSMGNGYTFELESLIFASLARSVCEILDLDSSEVTVYGDDI
ILPSCAVPALREVFKYVGFTTNTKKTFSEGPFRESCGKHYYSGVDVTPFYIRHRIVSPAD
LILVLNNLYRWATIDGVWDPRAHSVYLKYRKLLPKQLQRNTIPDGYGDGALVGSVLINPF
AKNRGWIRYVPVITDHTRDRERAELGSYLYDLFSRCLSESNDGLPLRGPSGCDSADLFAI
DQLICRSNPTKISRSTGKFDIQYIACSSRVLAPYGVFQGTKVASLHEAHHHHHH

Sequence of entity 4 (D, H), FASTA

>4Q7J_4 30S ribosomal protein S1 (chains D, H)
MTESFAQLFEESLKEIETRPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFKNAQGEL
EIQVGDEVDVALDAVEDGFGETLLSREKAKRHEAWITLEKAYEDAETVTGVINGKVKGGF
TVELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRRAVIESENSA
ERDQLLENLQEGMEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVNVGDE
ITVKVLKFDRERTRVSLGLKQLGEDPWVAIAKRLEHHHHHH

Primary citation

Molecular insights into replication initiation by Q beta replicase using ribosomal protein S1. Takeshita, D., Yamashita, S., Tomita, K. Nucleic Acids Res (2014) 42:10809-10822. DOI 10.1093/nar/gku745 · PubMed

Other PDB entries of the same protein (UniProt P0A6P1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PC3 1.83 Å, Elongation factor Tu:Ts complex with partially bound GDP
1EFU 2.5 Å, Elongation factor complex ef-tu/ef-ts from escherichia coli
3MMP 2.5 Å, Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and…
4R71 3.21 Å, Structure of the Qbeta holoenzyme complex in the P1211 crystal form
4PC7 3.6 Å, Elongation factor Tu:Ts complex in a near GTP conformation.

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