3VNV: Complex structure of viral RNA polymerase II

Complex structure of viral RNA polymerase II. Determined by X-ray diffraction at 2.6 Å resolution. Released 8 Aug 2012.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Escherichia coli O157:H7, Escherichia phage Qbeta
Chains: 3
Atoms: 9,680
Mol. weight: 146.74 kDa
Ligands: CH1, CA
Released: 8 Aug 2012

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

Secondary structure: helices and β-sheets

3VNV contains 59 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: 59 helices, 62 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	20-28	9
α-helix	34-42	9
α-helix	45-49	5
β-strand	59-67	9	1
β-strand	70-78	9	1
α-helix	81-84	4
α-helix	87-101	15
α-helix	108-113	6
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	183-185	3
α-helix	195-203	9
α-helix	209-226	18
β-strand	228	1	3
α-helix	229-231	3
β-strand	233	1	4
β-strand	241	1	4
α-helix	242-247	6
β-strand	252-260	9	2
α-helix	273-280	8
α-helix	281-283	3
β-strand	296-303	8	5
α-helix	309-322	14
β-strand	352-356	5	5
β-strand	359-365	7	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	422-424	3
α-helix	428-444	17
α-helix	449-451	3
β-strand	454-456	3	5
α-helix	459-463	5
α-helix	470-483	14
α-helix	485-487	3
α-helix	490-492	3
α-helix	494-495	2
β-strand	496-498	3	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	526-530	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
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	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	863-866	4
α-helix	870	1
β-strand	871-873	3	12
α-helix	875-877	3
α-helix	878-885	8
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	921-937	17
α-helix	938-941	4
α-helix	949-961	13
β-strand	964-967	4	14
β-strand	969	1	15
α-helix	972-974	3
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	1022-1040	19
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	1113-1127	15
β-strand	1128-1129	2	18
β-strand	1132-1133	2	18
α-helix	1134	1
α-helix	1135-1145	11
α-helix	1150-1154	5
β-strand	1156-1157	2	19
β-strand	1166-1167	2	19
α-helix	1170-1172	3
β-strand	1177-1179	3	20
β-strand	1182-1194	13	20
α-helix	1199-1214	16
α-helix	1237-1239	3
α-helix	1243-1245	3
β-strand	1248-1261	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(cpcpcpupapcp*c)-3')	G	RNA	7
RNA (5'-r(gpgpgpupapgpgpg)-3')	T	RNA	8

Sequence of entity 1 (A), FASTA

>3VNV_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

>3VNV_2 RNA (5'-R(*CP*CP*CP*UP*AP*CP*C)-3') (chains G)
CCCUACC

Sequence of entity 3 (T), FASTA

>3VNV_3 RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3') (chains T)
GGGUAGGG

Ligands and cofactors

ID	Name	Formula	Copies
CH1	3'-deoxy-cytidine-5'-triphosphate	C9 H16 N3 O13 P3	1
CA	Calcium ion	Ca	2

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
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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