3AVW: Viral RNA polymerase complex 4

Structure of viral RNA polymerase complex 4. Determined by X-ray diffraction at 2.6 Å resolution. Released 18 Jan 2012.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta
Chains: 3
Atoms: 9,843
Mol. weight: 148.36 kDa
Ligands: CA, GH3
Released: 18 Jan 2012

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

Secondary structure: helices and β-sheets

3AVW contains 56 α-helices and 62 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: 56 helices, 62 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	20-28	9
α-helix	34-52	19
β-strand	59-67	9	1
β-strand	70-78	9	1
α-helix	81-84	4
α-helix	87-102	16
α-helix	108-114	7
α-helix	116-126	11
β-strand	131-139	9	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	190-201	12
α-helix	209-226	18
β-strand	228	1	3
β-strand	233-234	2	4
β-strand	237-241	5	4
α-helix	242-247	6
β-strand	252-260	9	2
α-helix	272-277	6
α-helix	281-284	4
α-helix	294-295	2
β-strand	296-303	8	5
α-helix	305-307	3
α-helix	309-322	14
β-strand	352-356	5	5
β-strand	359-365	7	5
α-helix	369-378	10
β-strand	385-391	7	5
α-helix	400-409	10
β-strand	415-420	6	5
α-helix	428-444	17
α-helix	449-451	3
β-strand	454-456	3	5
α-helix	459-463	5
α-helix	467-482	16
α-helix	485-489	5
α-helix	490-492	3
α-helix	494-495	2
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	540-544	5	7
β-strand	549-550	2	7
β-strand	552-554	3	8
β-strand	558-563	6	7
α-helix	568-570	3
β-strand	573	1	9
β-strand	575	1	9
β-strand	576-578	3	6
β-strand	585-595	11	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	640-652	13	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	743-745	3
α-helix	750-752	3
α-helix	757-768	12
α-helix	784-803	20
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	871-873	3	12
α-helix	878-887	10
β-strand	894-897	4	12
β-strand	900-909	10	13
β-strand	912-918	7	13
α-helix	919-920	2
α-helix	921-938	18
α-helix	939-941	3
α-helix	948-961	14
β-strand	964-967	4	14
β-strand	969	1	15
β-strand	977	1	16
α-helix	978-984	7
α-helix	987-996	10
β-strand	1000-1002	3	13
β-strand	1008-1010	3	13
β-strand	1013	1	16
α-helix	1022-1041	20
α-helix	1045-1047	3
β-strand	1049-1051	3	14
β-strand	1054-1058	5	14
α-helix	1059-1061	3
α-helix	1062-1072	11
β-strand	1076	1	15
β-strand	1082	1	14
β-strand	1087-1090	4	17
β-strand	1093-1096	4	17
β-strand	1099-1100	2	17
α-helix	1113-1127	15
β-strand	1128-1129	2	18
β-strand	1132-1133	2	18
α-helix	1135-1144	10
α-helix	1145-1147	3
α-helix	1150-1154	5
β-strand	1156-1157	2	19
β-strand	1166-1167	2	19
β-strand	1177-1179	3	20
β-strand	1182-1195	14	20
α-helix	1199-1214	16
α-helix	1237-1239	3
β-strand	1247-1261	15	20

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(gpgpgpupcpcpapc)-3')	G	RNA	8
RNA (5'-r(apupcpgpupgpgpapcpcpcpa)-3')	T	RNA	12

Sequence of entity 1 (A), FASTA

>3AVW_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 (G), FASTA

>3AVW_2 RNA (5'-R(*GP*GP*GP*UP*CP*CP*AP*C)-3') (chains G)
GGGUCCAC

Sequence of entity 3 (T), FASTA

>3AVW_3 RNA (5'-R(*AP*UP*CP*GP*UP*GP*GP*AP*CP*CP*CP*A)-3') (chains T)
AUCGUGGACCCA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
GH3	3'-deoxy-guanosine-5'-triphosphate	C10 H16 N5 O13 P3	1

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
3VNV 2.6 Å, Complex structure of viral RNA polymerase II
3AVT 2.61 Å, Structure of viral RNA polymerase complex 1
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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