3VNU: Complex structure of viral RNA polymerase I

Complex structure of viral RNA polymerase I. Determined by X-ray diffraction at 3.2 Å resolution. Released 8 Aug 2012.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Escherichia coli O157:H7, Escherichia phage Qbeta
Chains: 3
Atoms: 9,584
Mol. weight: 147.09 kDa
Ligands: CA, ATP
Released: 8 Aug 2012

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

Secondary structure: helices and β-sheets

3VNU contains 54 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: 54 helices, 63 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	21-24	4
α-helix	35-43	9
α-helix	46-51	6
β-strand	64-66	3	1
β-strand	70-77	8	1
α-helix	81-84	4
α-helix	89-93	5
α-helix	99-102	4
α-helix	108-114	7
α-helix	116-123	8
β-strand	131-139	9	1
β-strand	142-144	3	2
β-strand	147-148	2	2
β-strand	152-158	7	2
α-helix	166-176	11
α-helix	188-205	18
α-helix	209-227	19
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-248	7
β-strand	255-260	6	2
α-helix	272-284	13
β-strand	296-303	8	4
α-helix	305-307	3
α-helix	309-322	14
β-strand	351-352	2	4
β-strand	355	1	4
β-strand	360-365	6	4
α-helix	370-376	7
β-strand	385-391	7	4
α-helix	400-408	9
β-strand	416-420	5	4
α-helix	428-443	16
α-helix	449-451	3
β-strand	454-456	3	4
α-helix	459-463	5
α-helix	467-477	11
α-helix	485-487	3
β-strand	496-498	3	5
β-strand	501-505	5	6
β-strand	509-516	8	6
β-strand	518	1	5
β-strand	521-522	2	7
β-strand	526-530	5	5
β-strand	536-539	4	5
β-strand	540-544	5	6
β-strand	552-553	2	7
β-strand	557-563	7	6
α-helix	568-570	3
β-strand	573	1	8
β-strand	575	1	8
β-strand	576-578	3	5
β-strand	584-595	12	9
α-helix	596	1
α-helix	598-600	3
β-strand	607	1	10
β-strand	614	1	9
β-strand	623-625	3	9
β-strand	635	1	10
β-strand	640-653	14	9
β-strand	658-663	6	9
β-strand	666-676	11	9
α-helix	703-713	11
α-helix	723-732	10
α-helix	733-735	3
α-helix	737-740	4
α-helix	745-747	3
α-helix	757-769	13
α-helix	784-803	20
α-helix	817-833	17
α-helix	840-843	4
α-helix	864-867	4
β-strand	873	1	11
α-helix	875-877	3
α-helix	878-885	8
β-strand	897	1	11
β-strand	902-903	2	12
β-strand	907	1	13
β-strand	913	1	13
β-strand	917-918	2	12
α-helix	921-936	16
α-helix	937-939	3
α-helix	949-961	13
β-strand	964-967	4	14
β-strand	969	1	15
α-helix	972-975	4
β-strand	977	1	16
α-helix	978-984	7
α-helix	987-995	9
β-strand	1000-1002	3	12
β-strand	1008-1010	3	12
β-strand	1013	1	16
α-helix	1022-1039	18
α-helix	1045-1047	3
β-strand	1049-1051	3	14
β-strand	1054-1058	5	14
α-helix	1059-1061	3
α-helix	1062-1071	10
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	1109-1110	2
α-helix	1113-1126	14
β-strand	1128-1129	2	18
β-strand	1132-1133	2	18
α-helix	1135-1145	11
α-helix	1151-1154	4
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	1199-1212	14
α-helix	1242-1245	4
β-strand	1247-1260	14	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, Escherichia phage Qbeta	P0A6N3 (AlphaFold model), P0A6P3 (AlphaFold model), P14647
RNA (5'-r(cpcpcpupapcpcpc)-3')	G	RNA	8
RNA (5'-r(gpgpgpupapgpgpg)-3')	T	RNA	8

Sequence of entity 1 (A), FASTA

>3VNU_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

>3VNU_2 RNA (5'-R(*CP*CP*CP*UP*AP*CP*CP*C)-3') (chains G)
CCCUACCC

Sequence of entity 3 (T), FASTA

>3VNU_3 RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3') (chains T)
GGGUAGGG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Mechanism for template-independent terminal adenylation activity of Q beta replicase. Takeshita, D., Yamashita, S., Tomita, K. Structure (2012) 20:1661-1669. DOI 10.1016/j.str.2012.07.004 · 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
3AVV 3.12 Å, Structure of viral RNA polymerase complex 3
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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