3AVU: Viral RNA polymerase complex 2

Structure of viral RNA polymerase complex 2. Determined by X-ray diffraction at 2.91 Å resolution. Released 18 Jan 2012.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta
Chains: 3
Atoms: 9,635
Mol. weight: 147.55 kDa
Ligands: CA
Released: 18 Jan 2012

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

Secondary structure: helices and β-sheets

3AVU contains 52 α-helices and 63 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: 52 helices, 63 β-strands

Element	Residues	Length	Sheet
α-helix	10-14	5
α-helix	20-24	5
α-helix	34-42	9
α-helix	46-49	4
α-helix	50-52	3
β-strand	59-67	9	1
β-strand	70-78	9	1
α-helix	81-84	4
α-helix	88-101	14
α-helix	111-114	4
α-helix	116-126	11
β-strand	131-139	9	1
β-strand	143-144	2	2
β-strand	147-148	2	2
β-strand	152-157	6	2
α-helix	163-176	14
β-strand	180	1	3
α-helix	190-204	15
α-helix	209-227	19
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	255-260	6	2
α-helix	273-284	12
β-strand	296-303	8	5
α-helix	309-318	10
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	400-410	11
β-strand	415-420	6	5
α-helix	428-430	3
α-helix	431-443	13
β-strand	454-456	3	5
α-helix	459-463	5
α-helix	467-480	14
α-helix	485-486	2
α-helix	490-492	3
α-helix	494-495	2
β-strand	496	1	6
β-strand	501-504	4	7
β-strand	510-515	6	7
β-strand	518	1	6
β-strand	520-522	3	8
β-strand	526-529	4	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	558-563	6	7
β-strand	578	1	6
β-strand	585-595	11	9
α-helix	598-600	3
β-strand	607	1	10
β-strand	614-616	3	9
β-strand	623-627	5	9
β-strand	635	1	10
β-strand	640-652	13	9
β-strand	658-663	6	9
β-strand	666-675	10	9
α-helix	703-713	11
α-helix	723-735	13
α-helix	738-740	3
α-helix	743-746	4
α-helix	757-768	12
α-helix	784-803	20
α-helix	817-833	17
α-helix	839-844	6
α-helix	858-860	3
α-helix	863-868	6
β-strand	871	1	11
α-helix	875-877	3
α-helix	878-885	8
β-strand	894	1	11
β-strand	900-906	7	12
β-strand	914-918	5	12
α-helix	921-937	17
α-helix	938-940	3
α-helix	950-961	12
β-strand	964-968	5	13
β-strand	969	1	14
β-strand	977	1	15
α-helix	978-984	7
α-helix	987-996	10
β-strand	1000-1002	3	12
β-strand	1008-1010	3	12
β-strand	1013	1	15
β-strand	1017	1	16
β-strand	1019	1	16
α-helix	1022-1040	19
α-helix	1045-1047	3
β-strand	1049-1051	3	13
β-strand	1054-1058	5	13
α-helix	1062-1071	10
β-strand	1076	1	14
α-helix	1078-1080	3
β-strand	1082	1	13
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	1	18
β-strand	1133	1	18
α-helix	1135-1144	10
α-helix	1145-1147	3
α-helix	1150-1153	4
β-strand	1156-1157	2	19
β-strand	1166-1167	2	19
β-strand	1178	1	20
β-strand	1183-1195	13	20
α-helix	1199-1214	16
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(gpgpgpupcpcp*a)-3')	G	RNA	7
RNA (5'-r(apupcpgpupgpgpapcpcpcpa)-3')	T	RNA	12

Sequence of entity 1 (A), FASTA

>3AVU_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

>3AVU_2 RNA (5'-R(*GP*GP*GP*UP*CP*CP*A)-3') (chains G)
GGGUCCA

Sequence of entity 3 (T), FASTA

>3AVU_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

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
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
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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