3AGQ: Viral polymerase form II

Structure of viral polymerase form II. Determined by X-ray diffraction at 3.22 Å resolution. Released 1 Sept 2010.

Method: X-ray diffraction
Resolution: 3.22 Å
Organisms: Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta
Chains: 1
Atoms: 9,257
Mol. weight: 141.44 kDa
Ligands: MG
Released: 1 Sept 2010

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

Secondary structure: helices and β-sheets

3AGQ contains 46 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: 46 helices, 63 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	34-43	10
α-helix	46-52	7
β-strand	60-67	8	1
β-strand	70-77	8	1
α-helix	81-84	4
α-helix	87-101	15
α-helix	109-114	6
α-helix	116-123	8
β-strand	132-139	8	1
β-strand	143-148	6	2
β-strand	152-157	6	2
α-helix	163-174	12
β-strand	180	1	3
α-helix	198-201	4
α-helix	209-226	18
β-strand	228	1	3
β-strand	233	1	4
β-strand	241	1	4
α-helix	242-248	7
β-strand	255-260	6	2
α-helix	268-270	3
α-helix	272-277	6
α-helix	283-285	3
β-strand	298-303	6	5
α-helix	309-319	11
β-strand	352-355	4	5
β-strand	360-365	6	5
α-helix	369-378	10
β-strand	385-391	7	5
α-helix	398-400	3
α-helix	401-409	9
β-strand	414-415	2	5
β-strand	417-420	4	5
α-helix	431-441	11
α-helix	443-445	3
β-strand	454-456	3	5
α-helix	467-482	16
α-helix	485-489	5
α-helix	490-492	3
β-strand	496-498	3	6
β-strand	501-503	3	7
β-strand	511-513	3	7
β-strand	518	1	6
β-strand	520-522	3	8
β-strand	528-530	3	6
β-strand	536-537	2	6
β-strand	540-544	5	7
β-strand	549-550	2	7
β-strand	552-554	3	8
β-strand	560-563	4	7
β-strand	573	1	9
β-strand	575	1	9
β-strand	576-578	3	6
β-strand	584-595	12	10
β-strand	607	1	11
β-strand	614-616	3	10
β-strand	623-627	5	10
β-strand	635	1	11
β-strand	640-653	14	10
β-strand	658-663	6	10
β-strand	666-675	10	10
α-helix	706-714	9
α-helix	723-734	12
α-helix	757-768	12
α-helix	784-803	20
α-helix	817-833	17
α-helix	842-845	4
α-helix	858-860	3
α-helix	864-867	4
β-strand	871	1	12
α-helix	878-885	8
β-strand	894	1	12
β-strand	900-907	8	13
β-strand	913-918	6	13
α-helix	921-937	17
α-helix	938-941	4
α-helix	949-961	13
β-strand	964-968	5	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	1022-1040	19
α-helix	1045-1047	3
β-strand	1049-1051	3	14
β-strand	1054-1058	5	14
α-helix	1061-1072	12
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	1113-1125	13
α-helix	1135-1144	10
α-helix	1145-1147	3
α-helix	1151-1154	4
β-strand	1156-1157	2	18
β-strand	1166-1167	2	18
β-strand	1177-1179	3	19
β-strand	1182-1184	3	19
β-strand	1186-1195	10	20
α-helix	1201-1214	14
α-helix	1237-1239	3
β-strand	1247-1258	12	20
β-strand	1261	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Ts, Elongation factor Tu 1, LINKER, Q beta replicase	A	protein	1289	Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta	P0A6N3 (AlphaFold model), P0A6P3 (AlphaFold model), P14647

Sequence of entity 1 (A), FASTA

>3AGQ_1 Elongation factor Ts, Elongation factor Tu 1, 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

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Assembly of Q{beta} viral RNA polymerase with host translational elongation factors EF-Tu and -Ts. Takeshita, D., Tomita, K. Proc Natl Acad Sci U S A (2010) 107:15733-15738. DOI 10.1073/pnas.1006559107 · 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
3VNU 3.2 Å, Complex structure of viral RNA polymerase I
4FWT 3.2 Å, Complex structure of viral RNA polymerase form III

Browse structure collections

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