3AGP: Viral polymerase form I

Structure of viral polymerase form I. Determined by X-ray diffraction at 2.8 Å resolution. Released 1 Sept 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Escherichia coli O157:H7, synthetic construct, Escherichia phage Qbeta
Chains: 1
Atoms: 9,311
Mol. weight: 141.46 kDa
Ligands: CA
Released: 1 Sept 2010

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

Secondary structure: helices and β-sheets

3AGP contains 51 α-helices and 64 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: 51 helices, 64 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	21-28	8
α-helix	34-43	10
α-helix	46-52	7
β-strand	59-67	9	1
β-strand	70-78	9	1
α-helix	81-84	4
α-helix	87-102	16
α-helix	108-126	19
β-strand	131-139	9	1
β-strand	142-148	7	2
β-strand	152-158	7	2
α-helix	163-174	12
β-strand	180	1	3
α-helix	183-185	3
α-helix	188-204	17
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	242-248	7
β-strand	255-260	6	2
α-helix	272-277	6
β-strand	296-303	8	5
α-helix	309-322	14
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	414-420	7	5
α-helix	422-424	3
α-helix	428-444	17
β-strand	454-456	3	5
α-helix	467-482	16
α-helix	485-489	5
β-strand	496-498	3	6
β-strand	501-505	5	7
β-strand	509-515	7	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
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	614-617	4	10
β-strand	620-627	8	10
β-strand	635	1	11
β-strand	640-652	13	10
β-strand	658-663	6	10
β-strand	666-677	12	10
α-helix	706-713	8
α-helix	723-733	11
α-helix	738-740	3
α-helix	743-746	4
α-helix	750-752	3
α-helix	757-768	12
α-helix	784-803	20
α-helix	817-833	17
α-helix	839-845	7
α-helix	858-860	3
α-helix	864-868	5
α-helix	870	1
β-strand	871	1	12
α-helix	875-877	3
α-helix	878-885	8
β-strand	894	1	12
β-strand	900-907	8	13
β-strand	913-918	6	13
α-helix	919-920	2
α-helix	921-937	17
α-helix	938-941	4
α-helix	949-960	12
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
β-strand	1017	1	17
β-strand	1019	1	17
α-helix	1022-1041	20
α-helix	1045-1047	3
β-strand	1049-1051	3	14
β-strand	1054-1058	5	14
α-helix	1059-1061	3
α-helix	1062-1072	11
β-strand	1076	1	15
β-strand	1082	1	14
β-strand	1087-1090	4	18
β-strand	1093-1096	4	18
β-strand	1099-1100	2	18
α-helix	1113-1125	13
β-strand	1128	1	19
β-strand	1133	1	19
α-helix	1135-1145	11
α-helix	1150-1153	4
β-strand	1156-1157	2	20
β-strand	1166-1167	2	20
β-strand	1177-1179	3	21
β-strand	1182-1195	14	21
α-helix	1199-1214	16
α-helix	1237-1239	3
α-helix	1243-1245	3
β-strand	1247-1261	15	21

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

Sequence of entity 1 (A), FASTA

>3AGP_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

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	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
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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