3AVT: Viral RNA polymerase complex 1

Structure of viral RNA polymerase complex 1. Determined by X-ray diffraction at 2.61 Å resolution. Released 18 Jan 2012.

Method: X-ray diffraction
Resolution: 2.61 Å
Organisms: Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta
Chains: 2
Atoms: 9,495
Mol. weight: 144.69 kDa
Ligands: CA, GH3
Released: 18 Jan 2012

Explore 3AVT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AVT contains 54 α-helices and 66 β-strands across 1 chain. 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: 54 helices, 66 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	34-42	9
α-helix	46-50	5
β-strand	61-67	7	1
β-strand	70-76	7	1
α-helix	81-84	4
α-helix	87-101	15
α-helix	108-125	18
β-strand	134-139	6	1
β-strand	142-148	7	2
β-strand	152-159	8	2
α-helix	163-176	14
β-strand	180	1	3
α-helix	183-185	3
α-helix	195-203	9
α-helix	209-225	17
β-strand	228	1	3
α-helix	229-231	3
β-strand	233-234	2	4
β-strand	237-241	5	4
α-helix	242-249	8
β-strand	252-260	9	2
α-helix	273-280	8
α-helix	281-283	3
β-strand	296-303	8	5
α-helix	309-323	15
β-strand	352-355	4	5
β-strand	360-365	6	5
α-helix	369-377	9
β-strand	385-391	7	5
α-helix	400-409	10
β-strand	414-420	7	5
α-helix	428-443	16
β-strand	454-456	3	5
α-helix	460-463	4
α-helix	467-482	16
α-helix	485-489	5
α-helix	490-492	3
β-strand	496-498	3	6
β-strand	501-505	5	7
β-strand	509-515	7	7
β-strand	518	1	6
β-strand	520-522	3	8
β-strand	526-530	5	6
β-strand	536-539	4	6
β-strand	542-544	3	7
β-strand	549-550	2	7
β-strand	552-554	3	8
β-strand	558-562	5	7
β-strand	573	1	9
β-strand	575	1	9
β-strand	576-578	3	6
β-strand	584-595	12	10
α-helix	596-597	2
β-strand	607	1	11
β-strand	614-616	3	10
β-strand	621-627	7	10
β-strand	635	1	11
β-strand	640-653	14	10
β-strand	658-663	6	10
β-strand	666-676	11	10
α-helix	703-713	11
α-helix	723-734	12
α-helix	738-740	3
α-helix	743-746	4
α-helix	757-768	12
α-helix	784-804	21
α-helix	817-833	17
α-helix	839-845	7
α-helix	858-860	3
α-helix	863-868	6
α-helix	870	1
β-strand	871	1	12
α-helix	878-887	10
β-strand	894	1	12
β-strand	900-903	4	13
β-strand	906-907	2	14
β-strand	913-914	2	14
β-strand	917-918	2	13
α-helix	919-920	2
α-helix	921-937	17
α-helix	938-941	4
α-helix	948-961	14
β-strand	964-968	5	15
β-strand	969	1	16
α-helix	972-974	3
β-strand	977	1	17
α-helix	978-984	7
α-helix	987-996	10
β-strand	1000-1002	3	13
β-strand	1009-1010	2	13
β-strand	1013	1	17
β-strand	1017	1	18
β-strand	1019	1	18
α-helix	1022-1041	20
α-helix	1045-1047	3
β-strand	1049-1051	3	15
β-strand	1054-1058	5	15
α-helix	1059-1061	3
α-helix	1062-1072	11
β-strand	1076	1	16
α-helix	1078-1080	3
β-strand	1082	1	15
β-strand	1087-1090	4	19
β-strand	1093-1096	4	19
β-strand	1099-1100	2	19
α-helix	1113-1127	15
β-strand	1128-1129	2	20
β-strand	1132-1133	2	20
α-helix	1135-1145	11
α-helix	1150-1154	5
β-strand	1156-1157	2	21
β-strand	1166-1167	2	21
α-helix	1170-1172	3
β-strand	1177-1179	3	22
β-strand	1182-1194	13	22
α-helix	1199-1213	15
α-helix	1237-1239	3
α-helix	1243-1245	3
β-strand	1248-1261	14	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase	A	protein	1289	Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta	P0A6N3 (AlphaFold model), P0A6P3 (AlphaFold model), P14647
RNA (5'-r(apupcpgpcpcp*a)-3')	T	RNA	7

Sequence of entity 1 (A), FASTA

>3AVT_1 Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase (chains A)
MAEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADG
VIKTKIDGNYGIILEVNCQTDFVAKDAGFQAFADKVLDAAVAGKITDVEVLKAQFEEERV
ALVAKIGENINIRRVAALEGDVLGSYQHGARIGVLVAAKGADEELVKHIAMHVAASKPEF
IKPEDVSAEVVEKEYQVQLDIAMQSGKPKEIAEKMVEGRMKKFTGEVSLTGQPFVMEPSK
TVGQLLKEHNAEVTGFIRFEVGEGIEKVETDFAAEVAAMSKQSHMSKEKFERTKPHVNVG
TIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRH
YAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLN
KCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFL
DSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTC
TGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDE
GGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFA
IREGGRTVGAGVVAKVLSGASGAAGGGGSGGGGSMSKTASSRNSLSAQLRRAANTRIEVE
GNLALSIANDLLLAYGQSPFNSEAECISFSPRFDGTPDDFRINYLKAEIMSKYDDFSLGI
DTEAVAWEKFLAAEAECALTNARLYRPDYSEDFNFSLGESCIHMARRKIAKLIGDVPSVE
GMLRHCRFSGGATTTNNRSYGHPSFKFALPQACTPRALKYVLALRASTHFDIRISDISPF
NKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGILRDRLRCWGIDLNDQTINQRRAHEGSV
TNNLATVDLSAASDSISLALCELLLPPGWFEVLMDLRSPKGRLPDGSVVTYEKISSMGNG
YTFELESLIFASLARSVCEILDLDSSEVTVYGDDIILPSCAVPALREVFKYVGFTTNTKK
TFSEGPFRESCGKHYYSGVDVTPFYIRHRIVSPADLILVLNNLYRWATIDGVWDPRAHSV
YLKYRKLLPKQLQRNTIPDGYGDGALVGSVLINPFAKNRGWIRYVPVITDHTRDRERAEL
GSYLYDLFSRCLSESNDGLPLRGPSGCDSADLFAIDQLICRSNPTKISRSTGKFDIQYIA
CSSRVLAPYGVFQGTKVASLHEAHHHHHH

Sequence of entity 2 (T), FASTA

>3AVT_2 RNA (5'-R(*AP*UP*CP*GP*CP*CP*A)-3') (chains T)
AUCGCCA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
GH3	3'-deoxy-guanosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Molecular basis for RNA polymerization by Q beta replicase. Takeshita, D., Tomita, K. Nat Struct Mol Biol (2012) 19:229-237. DOI 10.1038/nsmb.2204 · PubMed

Other PDB entries of the same protein (UniProt P0A6N3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3AVX 2.41 Å, Structure of viral RNA polymerase complex 5
3AVW 2.6 Å, Structure of viral RNA polymerase complex 4
3VNV 2.6 Å, Complex structure of viral RNA polymerase II
3AVY 2.62 Å, Structure of viral RNA polymerase complex 6
3AGP 2.8 Å, Structure of viral polymerase form I
3AVU 2.91 Å, Structure of viral RNA polymerase complex 2
3AVV 3.12 Å, Structure of viral RNA polymerase complex 3
3VNU 3.2 Å, Complex structure of viral RNA polymerase I
4FWT 3.2 Å, Complex structure of viral RNA polymerase form III
3AGQ 3.22 Å, Structure of viral polymerase form II

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