3AVV: Viral RNA polymerase complex 3

Structure of viral RNA polymerase complex 3. Determined by X-ray diffraction at 3.12 Å resolution. Released 18 Jan 2012.

Method: X-ray diffraction
Resolution: 3.12 Å
Organisms: Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta
Chains: 3
Atoms: 9,702
Mol. weight: 148.2 kDa
Ligands: CA
Released: 18 Jan 2012

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

Secondary structure: helices and β-sheets

3AVV contains 50 α-helices and 68 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: 50 helices, 68 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	21-24	4
α-helix	36-42	7
α-helix	46-50	5
β-strand	63-67	5	1
β-strand	70-74	5	1
β-strand	75-77	3	2
α-helix	81-84	4
α-helix	88-95	8
α-helix	98-101	4
α-helix	108-114	7
α-helix	120-123	4
β-strand	131-134	4	2
β-strand	137-139	3	1
β-strand	142-148	7	3
β-strand	152-158	7	3
α-helix	163-173	11
β-strand	180	1	4
α-helix	188-193	6
α-helix	200-203	4
α-helix	209-225	17
β-strand	228	1	4
β-strand	233	1	5
β-strand	241	1	5
α-helix	242-244	3
β-strand	255-260	6	3
α-helix	273-283	11
β-strand	296-303	8	6
α-helix	315-318	4
β-strand	352-355	4	6
β-strand	360-366	7	6
α-helix	370-378	9
β-strand	385-391	7	6
α-helix	400-408	9
β-strand	414-420	7	6
α-helix	428-442	15
β-strand	454-457	4	6
α-helix	459-464	6
α-helix	467-480	14
α-helix	494-495	2
β-strand	496	1	7
β-strand	498	1	8
β-strand	501-505	5	9
β-strand	509-515	7	9
β-strand	518	1	7
β-strand	520-522	3	10
α-helix	526-527	2
β-strand	528-530	3	8
β-strand	536-537	2	8
β-strand	540-544	5	9
β-strand	552-554	3	10
β-strand	558-563	6	9
β-strand	576-578	3	8
β-strand	585-594	10	11
α-helix	598-600	3
β-strand	607-608	2	12
β-strand	614-616	3	13
β-strand	623	1	13
β-strand	624-627	4	11
β-strand	634-635	2	12
β-strand	642-652	11	11
β-strand	660-663	4	13
β-strand	666-669	4	13
β-strand	670-673	4	11
α-helix	706-713	8
α-helix	723-734	12
α-helix	738-740	3
α-helix	745-747	3
α-helix	757-769	13
α-helix	784-803	20
α-helix	817-832	16
α-helix	839-842	4
α-helix	858-860	3
α-helix	864-868	5
β-strand	871	1	14
α-helix	878-885	8
β-strand	894	1	14
β-strand	900-903	4	15
β-strand	906-907	2	16
β-strand	913-914	2	16
β-strand	917-918	2	15
α-helix	921-937	17
α-helix	950-961	12
β-strand	964-967	4	17
β-strand	969	1	18
α-helix	972-975	4
β-strand	977	1	19
α-helix	978-982	5
α-helix	989-996	8
β-strand	1000-1002	3	15
β-strand	1008-1009	2	15
β-strand	1013	1	19
β-strand	1017	1	20
β-strand	1019	1	20
α-helix	1022-1040	19
α-helix	1045-1047	3
β-strand	1049-1051	3	17
β-strand	1054-1058	5	17
α-helix	1061-1071	11
β-strand	1076	1	18
α-helix	1078-1080	3
β-strand	1082	1	17
β-strand	1087-1090	4	21
β-strand	1093-1096	4	21
β-strand	1099-1100	2	21
α-helix	1113-1127	15
β-strand	1128-1129	2	22
β-strand	1132-1133	2	22
α-helix	1134	1
α-helix	1135-1145	11
α-helix	1150-1153	4
β-strand	1157	1	23
β-strand	1167	1	23
β-strand	1177-1179	3	24
β-strand	1182-1195	14	24
α-helix	1199-1214	16
α-helix	1237-1239	3
β-strand	1247-1261	15	24

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(gpgpgpupcpcpapu)-3')	G	RNA	8
RNA (5'-r(apapcpgpapupgpgpapcpcpcp*a)-3')	T	RNA	13

Sequence of entity 1 (A), FASTA

>3AVV_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

>3AVV_2 RNA (5'-R(*GP*GP*GP*UP*CP*CP*AP*U)-3') (chains G)
GGGUCCAU

Sequence of entity 3 (T), FASTA

>3AVV_3 RNA (5'-R(*AP*AP*CP*GP*AP*UP*GP*GP*AP*CP*CP*CP*A)-3') (chains T)
AACGAUGGACCCA

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
3AVU 2.91 Å, Structure of viral RNA polymerase complex 2
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

Browse structure collections

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