9GDA: RNAP-TopoI complex on duplex scaffold

Name: PDB 9GDA: RNAP-TopoI complex on duplex scaffold
Published: 2025-11-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RNAP-TopoI complex on duplex scaffold. Determined by electron microscopy at 2.7 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Escherichia coli, synthetic construct
Chains: 9
Atoms: 33,857
Mol. weight: 520.03 kDa
Ligands: MG, ZN
Released: 5 Nov 2025

Explore 9GDA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GDA contains 207 α-helices and 256 β-strands across 6 chains. 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: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12-18	7	1
β-strand	23-31	9	1
α-helix	35-50	16
β-strand	52-61	10	2
β-strand	74	1	3
α-helix	78-86	9
β-strand	90-92	3	4
β-strand	97-105	9	2
β-strand	108-111	4	3
α-helix	112-114	3
β-strand	115-116	2	2
α-helix	117-118	2
β-strand	121-123	3	4
β-strand	129-133	5	3
β-strand	139-150	12	2
β-strand	152-153	2	5
α-helix	155-158	4
α-helix	159-161	3
β-strand	170-172	3	2
β-strand	175-176	2	5
β-strand	180-189	10	1
β-strand	199-207	9	1
α-helix	213-233	21

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	6
β-strand	23-32	10	6
α-helix	35-49	15
β-strand	52-61	10	7
β-strand	74	1	8
α-helix	78-86	9
β-strand	90-92	3	9
β-strand	97-105	9	7
β-strand	108-111	4	8
α-helix	112-114	3
α-helix	116-117	2
β-strand	121-123	3	9
β-strand	129-133	5	8
β-strand	139-150	12	7
β-strand	152-153	2	10
α-helix	155-158	4
α-helix	161-163	3
β-strand	170-172	3	7
β-strand	175-176	2	10
β-strand	180-190	11	6
β-strand	197-207	11	6
α-helix	213-228	16

Chain C: 70 helices, 94 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	11-12	2
β-strand	13-14	2	11
α-helix	19-20	2
α-helix	23-26	4
α-helix	29-39	11
α-helix	48-56	9
β-strand	59-60	2	12
β-strand	66-75	10	12
α-helix	76-78	3
α-helix	82-88	7
β-strand	93-105	13	12
β-strand	114-128	15	12
α-helix	129-130	2
β-strand	136-137	2	13
β-strand	142-145	4	13
β-strand	147-151	5	14
α-helix	152	1
β-strand	154-159	6	15
α-helix	166-168	3
β-strand	172-177	6	15
β-strand	180	1	16
β-strand	184-188	5	15
β-strand	194-198	5	15
β-strand	204-205	2	15
α-helix	206-212	7
α-helix	217-224	8
β-strand	227-233	7	17
β-strand	236-240	5	17
α-helix	243-246	4
β-strand	250	1	18
β-strand	256-257	2	19
β-strand	260-261	2	19
β-strand	268	1	18
α-helix	271-280	10
β-strand	284-286	3	17
α-helix	289-292	4
α-helix	295	1
β-strand	296-297	2	17
β-strand	301-302	2	20
β-strand	309-311	3	20
α-helix	315	1
β-strand	316	1	17
α-helix	317	1
α-helix	319-328	10
β-strand	332-336	5	17
β-strand	339	1	21
β-strand	343	1	21
α-helix	346-353	8
α-helix	359-370	12
α-helix	378-389	12
β-strand	396	1	16
α-helix	399-408	10
α-helix	422-437	16
β-strand	451-454	4	14
α-helix	456-480	25
α-helix	489-491	3
α-helix	496-508	13
β-strand	512-514	3	13
α-helix	520-527	8
β-strand	529-531	3	14
α-helix	545-548	4
α-helix	552-554	3
β-strand	558	1	22
α-helix	566-568	3
β-strand	572-574	3	14
β-strand	575	1	22
β-strand	580-581	2	23
β-strand	587-595	9	23
β-strand	598-607	10	23
α-helix	608-613	6
β-strand	616-617	2	23
β-strand	623	1	24
β-strand	629	1	24
β-strand	633-636	4	23
β-strand	643-646	4	23
β-strand	652-654	3	23
α-helix	663-666	4
α-helix	671-673	3
β-strand	674	1	25
α-helix	676-686	11
α-helix	689-691	3
β-strand	700-701	2	11
α-helix	705-711	7
β-strand	716-717	2	26
β-strand	722-727	6	27
β-strand	731-736	6	27
α-helix	738-740	3
α-helix	742	1
β-strand	748-752	5	27
α-helix	753-754	2
β-strand	757-758	2	28
β-strand	763	1	29
β-strand	764-765	2	28
β-strand	768-769	2	26
β-strand	776-777	2	27
β-strand	782-785	4	26
β-strand	789-790	2	30
β-strand	793-794	2	30
β-strand	798-804	7	31
β-strand	816-819	4	31
α-helix	820-824	5
β-strand	830-841	12	29
β-strand	842-843	2	32
β-strand	846-847	2	32
β-strand	849-850	2	33
α-helix	859-862	4
β-strand	865	1	34
β-strand	870	1	35
β-strand	871	1	34
α-helix	872	1
β-strand	876-877	2	29
β-strand	882-884	3	35
β-strand	886-889	4	33
α-helix	897-906	10
β-strand	913-915	3	33
β-strand	918-919	2	35
α-helix	920-921	2
β-strand	926-935	10	29
β-strand	936	1	36
α-helix	940-941	2
α-helix	943-981	39
α-helix	986-991	6
α-helix	994-999	6
α-helix	1006-1037	32
β-strand	1040	1	36
α-helix	1042-1043	2
β-strand	1046-1058	13	29
β-strand	1065-1067	3	37
β-strand	1073-1075	3	37
β-strand	1076-1080	5	31
α-helix	1082-1084	3
β-strand	1087	1	38
α-helix	1092	1
β-strand	1093	1	38
α-helix	1094	1
β-strand	1096-1098	3	31
α-helix	1102-1106	5
β-strand	1108	1	25
α-helix	1110-1133	24
α-helix	1138-1150	13
α-helix	1161-1163	3
α-helix	1166-1175	10
β-strand	1182-1183	2	11
α-helix	1192-1201	10
β-strand	1209-1210	2	31
β-strand	1213	1	38
α-helix	1219	1
β-strand	1220	1	38
α-helix	1221	1
β-strand	1225-1232	8	31
β-strand	1233-1234	2	37
α-helix	1239-1241	3
β-strand	1244-1246	3	39
β-strand	1251	1	40
β-strand	1258	1	40
α-helix	1266-1268	3
β-strand	1269-1270	2	41
α-helix	1272-1280	9
α-helix	1284-1288	5
α-helix	1289-1296	8
α-helix	1298-1310	13
α-helix	1321-1331	11
β-strand	1335-1340	6	42

Chain D: 79 helices, 82 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	42
α-helix	25-26	2
α-helix	27-33	7
β-strand	34-37	4	43
β-strand	44	1	44
β-strand	51	1	44
α-helix	59-62	4
α-helix	78-80	3
α-helix	83	1
β-strand	84	1	45
α-helix	85	1
β-strand	91	1	45
α-helix	95-99	5
β-strand	102-112	11	43
α-helix	115-118	4
α-helix	123-128	6
α-helix	132-139	8
β-strand	144-149	6	46
β-strand	159-160	2	46
α-helix	162-172	11
β-strand	176-179	4	46
α-helix	181-190	10
α-helix	194-207	14
α-helix	211-230	20
α-helix	234-237	4
β-strand	238-244	7	43
α-helix	247-249	3
β-strand	252-254	3	47
β-strand	260-262	3	47
α-helix	264-284	21
α-helix	289-307	19
α-helix	315-316	2
β-strand	317	1	48
β-strand	323	1	48
α-helix	324-325	2
α-helix	327-331	5
α-helix	337-342	6
β-strand	345-346	2	41
β-strand	350-354	5	39
β-strand	355-357	3	49
β-strand	365-369	5	49
α-helix	370-376	7
α-helix	378-387	10
α-helix	394-403	10
α-helix	406-415	10
β-strand	421-424	4	39
α-helix	431-433	3
β-strand	434-437	4	39
β-strand	438-442	5	49
β-strand	447-449	3	49
α-helix	451-453	3
α-helix	454-457	4
β-strand	465-469	5	39
α-helix	474-479	6
α-helix	480-484	5
β-strand	485	1	39
α-helix	486-488	3
β-strand	491	1	50
β-strand	498	1	50
α-helix	505-513	9
β-strand	526-527	2	51
α-helix	530-539	10
β-strand	547-557	11	51
α-helix	562	1
β-strand	563-573	11	51
α-helix	574-580	7
α-helix	584	1
α-helix	589-591	3
α-helix	598-612	15
α-helix	614-635	22
α-helix	641-643	3
α-helix	645-647	3
α-helix	650-669	20
α-helix	675-702	28
β-strand	703-707	5	52
β-strand	713-717	5	52
α-helix	721-728	8
α-helix	734-741	8
β-strand	745	1	53
β-strand	748	1	54
α-helix	753	1
β-strand	754	1	54
α-helix	755	1
β-strand	759	1	53
α-helix	766-768	3
α-helix	769-804	36
β-strand	809-811	3	55
β-strand	820-822	3	56
β-strand	825-827	3	57
β-strand	830-833	4	57
α-helix	835-839	5
β-strand	843	1	58
β-strand	844	1	56
α-helix	847	1
β-strand	848-849	2	59
α-helix	850	1
β-strand	856-858	3	59
β-strand	863	1	58
α-helix	866-874	9
β-strand	880-882	3	56
α-helix	885-887	3
β-strand	894-895	2	55
α-helix	896-899	4
β-strand	901	1	60
β-strand	908	1	60
α-helix	909-910	2
α-helix	915-924	10
α-helix	925-929	5
β-strand	951	1	61
β-strand	956-961	6	62
β-strand	965-967	3	63
β-strand	973-975	3	63
β-strand	980-985	6	62
β-strand	991-997	7	62
α-helix	998	1
β-strand	1002-1003	2	63
β-strand	1010-1011	2	62
β-strand	1016	1	61
β-strand	1028	1	64
β-strand	1033-1038	6	65
β-strand	1042	1	66
β-strand	1046-1050	5	66
β-strand	1057-1061	5	66
α-helix	1062-1063	2
α-helix	1069-1071	3
β-strand	1077-1081	5	65
α-helix	1086	1
β-strand	1087	1	65
α-helix	1088	1
β-strand	1089	1	67
α-helix	1090	1
β-strand	1096	1	67
β-strand	1098-1100	3	65
β-strand	1106-1107	2	66
β-strand	1113-1115	3	65
β-strand	1120	1	64
α-helix	1138-1146	9
α-helix	1148-1150	3
α-helix	1153-1154	2
β-strand	1155-1156	2	68
β-strand	1161-1165	5	69
β-strand	1172-1178	7	69
β-strand	1186-1191	6	69
β-strand	1196	1	68
β-strand	1203-1204	2	69
β-strand	1209-1211	3	68
α-helix	1214-1216	3
α-helix	1217-1223	7
α-helix	1226-1244	19
α-helix	1250-1260	11
β-strand	1263-1268	6	70
β-strand	1279-1281	3	70
α-helix	1282-1294	13
α-helix	1297-1300	4
β-strand	1301-1305	5	70
α-helix	1309-1314	6
α-helix	1319-1325	7
α-helix	1328-1338	11
β-strand	1341-1342	2	42
α-helix	1347-1353	7
α-helix	1361-1375	15

Chain E: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-13	7
α-helix	16-31	16
α-helix	35-37	3
α-helix	46-55	10
α-helix	61-90	30

Chain F: 38 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	71
α-helix	11-21	11
β-strand	25-29	5	71
β-strand	36	1	72
α-helix	62-71	10
β-strand	74	1	73
β-strand	80	1	73
β-strand	84	1	72
α-helix	90-102	13
β-strand	106-108	3	71
α-helix	114-127	14
β-strand	134-136	3	71
α-helix	144-152	9
α-helix	154	1
β-strand	155	1	71
α-helix	156-157	2
α-helix	159-186	28
α-helix	195-213	19
β-strand	218-227	10	74
β-strand	233-241	9	74
β-strand	244-245	2	74
α-helix	251-263	13
β-strand	267-278	12	74
α-helix	279-283	5
β-strand	284	1	75
α-helix	285	1
α-helix	286-292	7
α-helix	293-297	5
α-helix	301-314	14
β-strand	317	1	76
α-helix	329-342	14
α-helix	345-347	3
β-strand	368	1	75
β-strand	370	1	76
α-helix	377-379	3
α-helix	385-400	16
α-helix	404-405	2
β-strand	406-417	12	74
β-strand	420-431	12	74
α-helix	453-454	2
β-strand	457-458	2	74
β-strand	460-461	2	74
β-strand	465-470	6	74
α-helix	471-478	8
α-helix	479-489	11
α-helix	497-506	10
β-strand	510-513	4	77
β-strand	516-519	4	77
α-helix	521-533	13
α-helix	535-538	4
α-helix	540-554	15
α-helix	560-579	20
β-strand	593-595	3	78
β-strand	606-611	6	78
β-strand	614-619	6	78
α-helix	620-623	4
α-helix	626-628	3
β-strand	633-635	3	78
β-strand	637-638	2	79
α-helix	639-641	3
α-helix	645-647	3
α-helix	650-658	9
β-strand	661	1	80
β-strand	668	1	80
β-strand	669-673	5	79
β-strand	678-683	6	79
β-strand	692-696	5	79
β-strand	709-710	2	81
β-strand	717-723	7	81
β-strand	726-731	6	81
β-strand	739-741	3	81
α-helix	752-755	4
β-strand	756-762	7	82
β-strand	769-774	6	82
β-strand	779-783	5	82
α-helix	786-789	4
β-strand	792-793	2	82
α-helix	794-795	2
β-strand	796	1	83
α-helix	797-802	6
α-helix	812-816	5
β-strand	820	1	84
β-strand	826	1	84
β-strand	827-832	6	83
β-strand	837-844	8	83
β-strand	847-855	9	83
β-strand	860-864	5	83

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase subunit alpha	A, B	protein	329	Escherichia coli	P0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	C	protein	1342	Escherichia coli	P0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'	D	protein	1415	Escherichia coli	P0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omega	E	protein	91	Escherichia coli	P0A800 (AlphaFold model)
DNA topoisomerase 1	F	protein	896	Escherichia coli	P06612
non-template DNA strand	N	DNA	39	synthetic construct
RNA	R	RNA	14	synthetic construct
template DNA strand	T	DNA	39	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9GDA_1 DNA-directed RNA polymerase subunit alpha (chains A, B)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE

Sequence of entity 2 (C), FASTA

>9GDA_2 DNA-directed RNA polymerase subunit beta (chains C)
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQ
SYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ
EVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRL
SALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTR
ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV
VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERG
DVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVS
RDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDE
LKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKIN
PIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAK
LREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMP
ESFNVLLKEIRSLGINIELEDE

Sequence of entity 3 (D), FASTA

>9GDA_3 DNA-directed RNA polymerase subunit beta' (chains D)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQ

Sequence of entity 4 (E), FASTA

>9GDA_4 DNA-directed RNA polymerase subunit omega (chains E)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR

Sequence of entity 5 (F), FASTA

>9GDA_5 DNA topoisomerase 1 (chains F)
GPWSHPQFEKGGGSGGGSGGSAWSHPQFEKHMGKALVIVESPAKAKTINKYLGSDYVVKS
SVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGK
EKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQ
AFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVERER
EIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVL
EREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQ
DAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQK
LYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRI
LPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGY
VRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFS
DFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALPPKER
CKTTINLVPENEVLNVLEGEDAETNALRAKRRCPKCGTAMDSYLIDPKRKLHVCGNNPTC
DGYEIEEGEFRIKGYDGPIVECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRNGEVA
PPKEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYRFRDRLPE
KLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGKATGWSAFYVDGKWVEGKK

Sequence of entity 6 (N), FASTA

>9GDA_6 non-template DNA strand (chains N)
GGTCAGTACGTCCTATCGATCTTCGGAAGAGATTCAGAG

Sequence of entity 7 (R), FASTA

>9GDA_7 RNA (chains R)
GAGUCCGCGGCGCG

Sequence of entity 8 (T), FASTA

>9GDA_8 template DNA strand (chains T)
CTCTGAATCTCTTCCGACGCGCCGCGGGACGTACTGACC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	5

Primary citation

DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation. Vidmar, V., Borde, C., Bruno, L. et al. Nat Struct Mol Biol (2026) 33:134-144. DOI 10.1038/s41594-025-01703-5 · PubMed

Other PDB entries of the same protein (UniProt P0A7Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3K4G 2.05 Å, Crystal structure of E. coli RNA polymerase alpha subunit C-terminal domain
8FVW 2.1 Å, CryoEM structure of E.coli transcription elongation complex bound to ppGpp
8FVR 2.42 Å, CryoEM structure of E.coli transcription elongation complex
9ZP4 2.42 Å, E. coli RNA polymerase elongation complex containing the unnatural dZ:PTP base pair in a…
8HKC 2.49 Å, Cryo-EM structure of E. coli RNAP sigma32 complex
1BDF 2.5 Å, Structure of escherichia coli RNA polymerase alpha subunit N-terminal domain
6XL5 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter open complex (EcmrR-RPo)
6XL9 2.5 Å, Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA…
12EC 2.6 Å, Half-translocated RNA polymerase elemental paused elongation complex, swiveled (ePEC…
8F1J 2.6 Å, SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2…
8PIB 2.6 Å, autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter…
9MSF 2.6 Å, de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic…

Browse structure collections

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