7RIM: DNA-directed RNA polymerase II subunit RPB1

RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1. Determined by X-ray diffraction at 2.9 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 13
Atoms: 29,191
Mol. weight: 489.82 kDa
Ligands: MG, ZN, 5N0
Released: 12 Jan 2022

Explore 7RIM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RIM contains 173 α-helices and 210 β-strands across 10 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: 77 helices, 69 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
β-strand	16-18	3	2
β-strand	21	1	3
α-helix	24-30	7
β-strand	34	1	4
β-strand	41	1	5
α-helix	42	1
α-helix	43-45	3
β-strand	49	1	5
α-helix	78-81	4
β-strand	82-90	9	4
α-helix	93-95	3
α-helix	96-104	9
α-helix	120-126	7
α-helix	131-142	12
β-strand	147	1	6
β-strand	170	1	6
β-strand	174-177	4	7
β-strand	180-183	4	7
β-strand	201	1	7
α-helix	204-212	9
α-helix	216-221	6
β-strand	225	1	8
β-strand	229	1	8
α-helix	231-233	3
β-strand	236-241	6	4
α-helix	242-243	2
α-helix	244-246	3
α-helix	261-281	21
α-helix	289-304	16
β-strand	315	1	9
α-helix	317-319	3
α-helix	320	1
β-strand	321	1	9
α-helix	322-324	3
α-helix	325-329	5
α-helix	335	1
α-helix	336-340	5
β-strand	343-345	3	10
β-strand	348-355	8	11
β-strand	363-367	5	11
α-helix	368-373	6
β-strand	375-379	5	12
α-helix	385-394	10
β-strand	402-406	5	12
β-strand	412-414	3	12
α-helix	419-421	3
β-strand	431-435	5	12
α-helix	436	1
β-strand	441-445	5	11
α-helix	452-454	3
β-strand	455-463	9	11
β-strand	468-470	3	11
α-helix	472-474	3
α-helix	475-478	4
β-strand	486-490	5	11
α-helix	495-500	6
α-helix	501-505	5
β-strand	506	1	11
α-helix	507-510	4
β-strand	512-513	2	13
α-helix	515-517	3
β-strand	518-519	2	13
α-helix	525-535	11
β-strand	540-541	2	14
α-helix	543-552	10
α-helix	560-563	4
β-strand	565	1	15
β-strand	571	1	15
β-strand	572-573	2	14
α-helix	574-579	6
α-helix	583	1
β-strand	588-590	3	16
β-strand	605-607	3	16
β-strand	612-614	3	16
α-helix	619-622	4
α-helix	629-636	8
α-helix	639-660	22
α-helix	666-669	4
α-helix	673-698	26
α-helix	710-736	27
α-helix	742-749	8
α-helix	755-758	4
α-helix	759-763	5
β-strand	766-767	2	17
β-strand	770	1	18
β-strand	773	1	18
β-strand	779	1	19
β-strand	782	1	19
β-strand	799-800	2	17
α-helix	810-845	36
β-strand	849-850	2	20
β-strand	856-857	2	20
β-strand	863-865	3	20
α-helix	868-870	3
β-strand	873	1	21
β-strand	879-882	4	22
α-helix	890-897	8
α-helix	908-909	2
β-strand	913	1	23
α-helix	923-946	24
β-strand	953-956	4	22
α-helix	960-970	11
β-strand	979	1	23
α-helix	983-995	13
α-helix	1005-1014	10
α-helix	1016-1025	10
α-helix	1028-1029	2
α-helix	1030-1034	5
α-helix	1039-1056	18
β-strand	1057	1	21
α-helix	1058-1059	2
α-helix	1064-1077	14
α-helix	1097-1105	9
β-strand	1116-1119	4	24
β-strand	1120	1	25
α-helix	1121	1
α-helix	1128-1138	11
β-strand	1141-1142	2	26
α-helix	1143-1146	4
β-strand	1147-1154	8	27
α-helix	1167-1172	6
β-strand	1191-1197	7	27
α-helix	1199-1204	6
α-helix	1209-1220	12
β-strand	1224-1228	5	27
β-strand	1236-1242	7	27
α-helix	1258-1270	13
β-strand	1272-1274	3	26
β-strand	1282-1287	6	24
β-strand	1290-1292	3	28
β-strand	1298-1300	3	28
β-strand	1303-1308	6	24
α-helix	1313-1317	5
β-strand	1322	1	25
β-strand	1328-1329	2	24
α-helix	1332-1339	8
α-helix	1341-1357	17
α-helix	1365-1376	12
α-helix	1389-1391	3
α-helix	1397-1400	4
α-helix	1405-1415	11
β-strand	1418-1419	2	2
α-helix	1424-1429	6
α-helix	1437-1439	3
β-strand	1441-1445	5	29

Chain B: 52 helices, 81 β-strands

Element	Residues	Length	Sheet
α-helix	23	1
β-strand	24	1	30
α-helix	25	1
α-helix	29-41	13
α-helix	45-53	9
α-helix	54-58	5
α-helix	59-64	6
β-strand	69-72	4	31
β-strand	87-97	11	31
β-strand	101-103	3	32
β-strand	109-111	3	32
α-helix	112-113	2
α-helix	114-119	6
β-strand	125-136	12	31
β-strand	164-171	8	31
α-helix	172-173	2
α-helix	180-183	4
α-helix	186-191	6
β-strand	203-205	3	33
β-strand	208-212	5	33
α-helix	213	1
β-strand	214-218	5	34
α-helix	219	1
β-strand	223-227	5	35
β-strand	234-243	10	35
β-strand	251-259	9	35
β-strand	269-271	3	35
β-strand	280-281	2	35
α-helix	282-288	7
α-helix	294-301	8
α-helix	308-320	13
α-helix	327-332	6
α-helix	346-358	13
α-helix	371-389	19
α-helix	401-403	3
β-strand	404-407	4	34
α-helix	409-434	26
α-helix	450-463	14
β-strand	480-482	3	33
α-helix	483-484	2
α-helix	488-494	7
β-strand	497-499	3	34
α-helix	509-512	4
α-helix	516-518	3
β-strand	522	1	36
β-strand	533	1	37
β-strand	536	1	37
β-strand	537-538	2	34
β-strand	539	1	36
β-strand	544-547	4	38
α-helix	552-560	9
β-strand	564-565	2	39
α-helix	571-573	3
β-strand	578-582	5	39
β-strand	586-590	5	39
α-helix	593-606	14
β-strand	614-618	5	39
β-strand	623-627	5	39
β-strand	630-639	10	38
β-strand	640-642	3	40
β-strand	649-651	3	40
β-strand	654	1	30
α-helix	655-666	12
α-helix	681-686	6
β-strand	690-694	5	38
α-helix	697-700	4
β-strand	703-704	2	38
α-helix	707-710	4
α-helix	728-729	2
β-strand	740-741	2	38
α-helix	745-748	4
α-helix	753-755	3
α-helix	759-761	3
β-strand	762	1	41
α-helix	764-774	11
β-strand	777	1	42
β-strand	792-796	5	43
β-strand	800	1	44
β-strand	804-805	2	45
α-helix	809-812	4
β-strand	820	1	44
β-strand	821-827	7	46
β-strand	839-842	4	46
α-helix	843-847	5
β-strand	853-862	10	43
β-strand	865	1	47
β-strand	871	1	47
β-strand	873-874	2	48
β-strand	882-883	2	48
β-strand	898	1	49
β-strand	904-905	2	43
β-strand	910-912	3	49
β-strand	914-917	4	48
β-strand	934-936	3	48
β-strand	939-940	2	49
α-helix	941-942	2
β-strand	947-956	10	43
β-strand	962-972	11	43
β-strand	980-982	3	46
β-strand	987-988	2	46
β-strand	990-994	5	46
β-strand	1001	1	50
β-strand	1010-1012	3	46
α-helix	1014-1016	3
β-strand	1022	1	41
α-helix	1023-1038	16
β-strand	1042-1043	2	45
α-helix	1052-1061	10
β-strand	1069-1070	2	46
β-strand	1073	1	50
α-helix	1079	1
β-strand	1080	1	50
α-helix	1081	1
β-strand	1085-1094	10	46
β-strand	1095	1	42
α-helix	1099-1102	4
β-strand	1104-1106	3	11
β-strand	1111	1	51
β-strand	1118	1	51
α-helix	1122-1124	3
α-helix	1127	1
β-strand	1128-1130	3	10
α-helix	1132-1141	10
α-helix	1144-1152	9
β-strand	1157-1163	7	1
β-strand	1172-1174	3	52
β-strand	1179-1181	3	52
β-strand	1182	1	53
β-strand	1187	1	53
β-strand	1191-1197	7	1
α-helix	1198-1209	12
β-strand	1212	1	3
β-strand	1215-1217	3	2

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	54
β-strand	17-23	7	54
α-helix	27-39	13
β-strand	43-54	12	55
α-helix	60-69	10
β-strand	72	1	56
α-helix	77-79	3
α-helix	81-82	2
β-strand	97-104	8	55
β-strand	111-114	4	57
α-helix	115-117	3
β-strand	119-120	2	55
α-helix	131	1
β-strand	132	1	56
α-helix	133	1
β-strand	143-147	5	57
β-strand	152-162	11	55
α-helix	168-170	3
β-strand	176-180	5	54
α-helix	197-200	4
α-helix	202-204	3
α-helix	205-207	3
α-helix	212-214	3
α-helix	218-219	2
β-strand	227-233	7	54
α-helix	240-265	26

Chain E: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
β-strand	28	1	58
α-helix	32-35	4
α-helix	39-46	8
β-strand	47	1	59
β-strand	53	1	59
β-strand	60-62	3	60
β-strand	64	1	58
α-helix	66-71	6
β-strand	78-81	4	60
β-strand	88	1	61
α-helix	90-102	13
β-strand	107-112	6	60
β-strand	116	1	61
α-helix	118-122	5
β-strand	131-136	6	60
α-helix	137-140	4
α-helix	144-146	3
α-helix	151	1
β-strand	152-155	4	62
α-helix	156-157	2
α-helix	158-167	10
α-helix	172-174	3
β-strand	177-178	2	62
α-helix	183-187	5
β-strand	195-202	8	62
β-strand	206-214	9	62

Chain F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	84	1	63
α-helix	85-86	2
α-helix	87-102	16
α-helix	117-126	10
β-strand	132-137	6	29
β-strand	143-147	5	29
β-strand	152	1	63

Chain H: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	15
β-strand	23-30	8	15
β-strand	37-43	7	15
β-strand	54-60	7	15
α-helix	77-79	3
α-helix	81-83	3
β-strand	95-97	3	15
β-strand	100-108	9	15
β-strand	111-118	8	15
β-strand	121-127	7	15
β-strand	142-145	4	15

Chain I: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	64
β-strand	13	1	64
β-strand	15-19	5	65
β-strand	24-28	5	65
β-strand	35-37	3	65
β-strand	42-47	6	27
α-helix	60-64	5
β-strand	70	1	66
α-helix	73-75	3
β-strand	83-87	5	66
β-strand	99-103	5	66
β-strand	109-111	3	66

Chain J: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	67
β-strand	13	1	67
α-helix	18-26	9
α-helix	32-38	7
α-helix	44-51	8
β-strand	53	1	44
α-helix	56-61	6

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA	R	RNA	9	synthetic construct
Template strand DNA	T	DNA	30	synthetic construct
Non-template DNA	N	DNA	20	synthetic construct
DNA-directed RNA polymerase II subunit RPB1	A	protein	1733	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P04050 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2	B	protein	1224	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P08518 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P16370 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20434 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	155	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20435
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	146	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20436
DNA-directed RNA polymerase II subunit RPB9	I	protein	122	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	70	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22139
DNA-directed RNA polymerase II subunit RPB11	K	protein	120	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38902

1 more molecules are not listed.

Sequence of entity 1 (R), FASTA

>7RIM_1 RNA (chains R)
AUCGAGAGG

Sequence of entity 2 (T), FASTA

>7RIM_2 Template strand DNA (chains T)
CCCTTCTCTCTGGTCATGAGCCTCTCGATG

Sequence of entity 3 (N), FASTA

>7RIM_3 Non-template DNA (chains N)
GTCATGACCAGAGAGAAGGG

Sequence of entity 4 (A), FASTA

>7RIM_4 DNA-directed RNA polymerase II subunit RPB1 (chains A)
MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS
IDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE
LMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK
LVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP
VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV
ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE
LDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR
AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA
DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF
IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP
KDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN
GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR
FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV
DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR
LVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD
LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI
RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC
LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT
LNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH
TTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA
AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML
KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP
GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG
LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA
FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS
NDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS
PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS
PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Sequence of entity 5 (B), FASTA

>7RIM_5 DNA-directed RNA polymerase II subunit RPB2 (chains B)
MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQ
DIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLR
NLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCY
LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI
RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH
ICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEF
LPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTL
FKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVS
QVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS
LMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETL
RTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAK
LMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEND
LDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGV
FLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI
MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIA
PGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG
LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR
MTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKK
LMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIA
HGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAA
KLLFQELMAMNITPRLYTDRSRDF

Sequence of entity 6 (C), FASTA

>7RIM_6 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 7 (E), FASTA

>7RIM_7 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 8 (F), FASTA

>7RIM_8 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 9 (H), FASTA

>7RIM_9 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 10 (I), FASTA

>7RIM_10 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 11 (J), FASTA

>7RIM_11 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 12 (K), FASTA

>7RIM_12 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	8
5N0	3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl…	C64 H75 N23 O12	1

Primary citation

RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Oh, J., Jia, T., Xu, J. et al. Proc Natl Acad Sci U S A (2022) 119. DOI 10.1073/pnas.2114065119 · PubMed

Other PDB entries of the same protein (UniProt P04050 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VKO 1.8 Å, SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493
9SV6 1.96 Å, CryoEM structure of transcribing RNA polymerase II elongation complex with ATP and Elf1
5VKL 2.2 Å, SPT6 tSH2-RPB1 1476-1500 pS1493
9W8V 2.23 Å, Structure of post-translocation state of yeast Pol II complexed with a cisplatin-induced…
9QEB 2.26 Å, CryoEM structure of transcribing RNA polymerase II elongation complex
1TWF 2.3 Å, RNA polymerase II complexed with UTP at 2.3 A resolution
9RYB 2.33 Å, CryoEM structure of transcribing RNA polymerase II elongation complex in post-catalysis…
9KD8 2.46 Å, The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin…
6NPW 2.49 Å, SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide
9K7F 2.5 Å, RNA polymerase II elongation complex apo structure.
30ES 2.54 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
30EP 2.55 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…

Browse structure collections

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