8K5P: DNA-directed RNA polymerase II subunit RPB1

Name: PDB 8K5P: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2)
Published: 2024-01-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2). Determined by electron microscopy at 2.8 Å resolution. Released 31 Jan 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Saccharomyces cerevisiae S288C, synthetic construct
Chains: 18
Atoms: 42,713
Mol. weight: 834.11 kDa
Ligands: ZN, MG
Released: 31 Jan 2024

Explore 8K5P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K5P contains 248 α-helices and 278 β-strands across 15 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: 78 helices, 77 β-strands

Element	Residues	Length	Sheet
α-helix	10	1
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	43	1	5
β-strand	47	1	5
α-helix	48-49	2
α-helix	56-58	3
α-helix	65-66	2
β-strand	67	1	6
β-strand	72	1	6
β-strand	83	1	4
β-strand	84-90	7	7
α-helix	93-95	3
α-helix	96-105	10
β-strand	106	1	8
β-strand	113	1	8
α-helix	120-126	7
α-helix	131-144	14
β-strand	147	1	9
β-strand	151-153	3	10
β-strand	161-163	3	10
α-helix	169	1
β-strand	170	1	9
α-helix	171-172	2
β-strand	173-177	5	11
β-strand	180-185	6	11
β-strand	198-202	5	11
α-helix	203	1
α-helix	204-212	9
α-helix	216-222	7
α-helix	231-234	4
β-strand	236-239	4	7
α-helix	248-250	3
α-helix	261-282	22
α-helix	286-304	19
α-helix	312-314	3
β-strand	315	1	12
α-helix	320	1
β-strand	321	1	12
α-helix	322	1
α-helix	325-328	4
α-helix	337-341	5
β-strand	343-344	2	13
β-strand	348-352	5	14
β-strand	353-355	3	15
β-strand	364-367	4	15
α-helix	368-373	6
β-strand	375-379	5	16
α-helix	385-394	10
β-strand	402-406	5	16
β-strand	412-414	3	16
β-strand	431-435	5	16
α-helix	436	1
β-strand	441-445	5	14
α-helix	452-454	3
β-strand	455-459	5	14
β-strand	460-463	4	15
β-strand	468-470	3	15
α-helix	472-474	3
α-helix	475-478	4
β-strand	486-490	5	14
α-helix	495-504	10
β-strand	506	1	14
α-helix	508-510	3
β-strand	512-513	2	17
β-strand	518-519	2	17
α-helix	526-535	10
β-strand	540-541	2	18
α-helix	543-552	10
α-helix	560-563	4
β-strand	565	1	19
β-strand	571	1	19
β-strand	572-573	2	18
α-helix	574-581	8
α-helix	583	1
β-strand	588-590	3	20
β-strand	605-608	4	20
β-strand	611-614	4	20
α-helix	619-622	4
α-helix	629-636	8
α-helix	639-658	20
β-strand	663	1	21
α-helix	666-669	4
α-helix	673-698	26
α-helix	704-705	2
α-helix	712-736	25
α-helix	742-749	8
α-helix	755-762	8
α-helix	765-768	4
β-strand	770	1	22
β-strand	773	1	22
β-strand	779	1	23
β-strand	782	1	23
α-helix	794-797	4
α-helix	810-844	35
β-strand	849-850	2	24
β-strand	856-857	2	24
β-strand	863-865	3	24
α-helix	868-870	3
β-strand	873	1	25
α-helix	875-877	3
β-strand	879-882	4	26
α-helix	890-897	8
α-helix	907-909	3
α-helix	910-912	3
β-strand	913	1	27
α-helix	924-946	23
β-strand	953-956	4	26
α-helix	960-971	12
α-helix	978	1
β-strand	979	1	27
α-helix	983-995	13
α-helix	1005-1013	9
α-helix	1016-1025	10
α-helix	1028-1033	6
α-helix	1039-1055	17
β-strand	1057	1	25
α-helix	1058-1059	2
α-helix	1064-1077	14
α-helix	1098-1106	9
β-strand	1116-1119	4	28
β-strand	1120	1	29
α-helix	1128-1133	6
β-strand	1140-1141	2	30
β-strand	1149-1151	3	31
β-strand	1154	1	32
α-helix	1167-1173	7
β-strand	1191	1	32
β-strand	1192	1	33
β-strand	1194-1195	2	31
α-helix	1199-1201	3
α-helix	1209-1220	12
β-strand	1224-1227	4	33
β-strand	1238	1	31
β-strand	1239-1242	4	33
α-helix	1258-1268	11
β-strand	1272-1274	3	30
β-strand	1282-1292	11	28
β-strand	1298-1308	11	28
α-helix	1313-1316	4
β-strand	1322	1	29
β-strand	1328-1329	2	28
α-helix	1333-1336	4
α-helix	1341-1356	16
α-helix	1365-1375	11
α-helix	1396-1402	7
α-helix	1405-1414	10
β-strand	1418-1419	2	2
α-helix	1424-1430	7
α-helix	1437-1440	4
β-strand	1441-1445	5	34
α-helix	1447-1453	7

Chain B: 54 helices, 72 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	23-25	3
α-helix	29-34	6
α-helix	38-41	4
α-helix	45-53	9
α-helix	54-58	5
α-helix	59-63	5
β-strand	71	1	35
β-strand	88-89	2	35
β-strand	92-97	6	36
β-strand	101-103	3	37
β-strand	109-111	3	37
α-helix	114-119	6
β-strand	125-132	8	36
β-strand	135-136	2	35
β-strand	164-171	8	36
α-helix	186-191	6
β-strand	203-205	3	38
β-strand	208-212	5	38
α-helix	213	1
β-strand	214-218	5	39
β-strand	223-227	5	40
β-strand	236-242	7	40
β-strand	252-258	7	40
β-strand	269-272	4	40
α-helix	279	1
β-strand	280-281	2	40
α-helix	282-288	7
α-helix	294-301	8
α-helix	308-320	13
α-helix	321-323	3
α-helix	327-336	10
α-helix	348-358	11
α-helix	371-389	19
α-helix	395-397	3
α-helix	401-403	3
β-strand	404-407	4	39
α-helix	411-435	25
α-helix	445-463	19
β-strand	480-482	3	38
α-helix	488-494	7
β-strand	497-499	3	39
α-helix	514-515	2
α-helix	516-518	3
β-strand	522	1	41
β-strand	536-538	3	39
β-strand	539	1	41
α-helix	540	1
β-strand	544-545	2	42
α-helix	552-560	9
β-strand	564-565	2	43
β-strand	578-582	5	43
β-strand	585-590	6	43
α-helix	593-605	13
β-strand	614-618	5	43
β-strand	623-627	5	43
β-strand	633-639	7	42
β-strand	640-643	4	44
β-strand	648-651	4	44
α-helix	655-667	13
α-helix	681-687	7
β-strand	690-694	5	42
α-helix	696-700	5
β-strand	703-704	2	42
α-helix	707-709	3
α-helix	728-729	2
β-strand	740-741	2	42
α-helix	745-748	4
α-helix	759-761	3
α-helix	764-774	11
β-strand	792-796	5	45
β-strand	800	1	46
β-strand	804-805	2	47
α-helix	808-810	3
β-strand	821-827	7	48
β-strand	828	1	21
β-strand	838-842	5	48
α-helix	843-847	5
β-strand	853-862	10	45
β-strand	865-866	2	49
β-strand	870-871	2	49
β-strand	873-874	2	50
β-strand	898	1	51
α-helix	899-900	2
β-strand	904-905	2	45
β-strand	910-912	3	51
β-strand	914-917	4	50
β-strand	934-936	3	50
β-strand	939-940	2	51
α-helix	941-942	2
β-strand	947-956	10	45
β-strand	962-972	11	45
β-strand	979-982	4	48
β-strand	987-994	8	48
β-strand	1001-1002	2	52
β-strand	1010-1012	3	48
α-helix	1014-1016	3
α-helix	1017-1020	4
α-helix	1023-1038	16
α-helix	1041	1
β-strand	1042-1043	2	47
α-helix	1052-1062	11
β-strand	1069-1070	2	48
β-strand	1072-1073	2	52
α-helix	1079	1
β-strand	1080	1	52
α-helix	1081	1
β-strand	1085-1086	2	48
β-strand	1089-1094	6	48
α-helix	1099-1101	3
β-strand	1104-1106	3	14
α-helix	1118-1119	2
β-strand	1129-1130	2	13
α-helix	1132-1141	10
α-helix	1144-1148	5
α-helix	1149-1153	5
β-strand	1158-1163	6	1
β-strand	1172-1174	3	53
β-strand	1179-1181	3	53
β-strand	1182	1	54
β-strand	1187	1	54
β-strand	1191-1196	6	1
α-helix	1198-1209	12
β-strand	1212	1	3
β-strand	1215-1217	3	2
α-helix	1221-1223	3

Chain C: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	55
β-strand	17-23	7	55
α-helix	27-39	13
β-strand	43-54	12	56
α-helix	60-68	9
β-strand	72-74	3	57
α-helix	77-79	3
β-strand	97-104	8	56
β-strand	111-114	4	58
α-helix	115-117	3
β-strand	119-120	2	56
β-strand	129-132	4	57
α-helix	133	1
β-strand	143-147	5	58
β-strand	152-162	11	56
α-helix	168-170	3
β-strand	173-180	8	55
α-helix	202-204	3
α-helix	207-209	3
α-helix	211-214	4
β-strand	228-234	7	55
α-helix	240-269	30

Chain D: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
β-strand	37	1	73
α-helix	38-39	2
β-strand	45	1	73
α-helix	46-48	3
α-helix	52-77	26
α-helix	119-130	12
α-helix	139-150	12
α-helix	157-167	11
α-helix	174-182	9
α-helix	188-194	7
α-helix	205-219	15

Chain E: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-26	25
α-helix	32-35	4
α-helix	39-46	8
β-strand	47	1	59
α-helix	52	1
β-strand	53	1	59
α-helix	54	1
β-strand	58-62	5	60
α-helix	68-71	4
β-strand	77-82	6	60
α-helix	90-102	13
β-strand	107-112	6	60
α-helix	118-123	6
β-strand	131-136	6	60
α-helix	137-140	4
β-strand	152-155	4	61
α-helix	158-168	11
β-strand	177-178	2	61
α-helix	183-188	6
β-strand	195-200	6	61
β-strand	208-214	7	61

Chain F: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	84	1	62
α-helix	87-102	16
α-helix	117-126	10
β-strand	132-137	6	34
α-helix	138	1
β-strand	143-147	5	34
β-strand	152	1	62

Chain G: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	74
β-strand	8-13	6	34
α-helix	15-17	3
α-helix	22-34	13
β-strand	38-39	2	74
β-strand	43-48	6	74
β-strand	55	1	34
α-helix	58	1
β-strand	59-61	3	34
α-helix	62	1
β-strand	68-73	6	34
β-strand	76-79	4	74
β-strand	85-94	10	75
β-strand	99-102	4	75
β-strand	108	1	75
β-strand	109	1	76
β-strand	120-122	3	77
β-strand	129-132	4	77
β-strand	135-136	2	77
β-strand	142-147	6	75
β-strand	160	1	76
β-strand	161-162	2	75

Chain H: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	19
β-strand	11-16	6	63
β-strand	23-29	7	63
β-strand	37-43	7	63
β-strand	54	1	63
β-strand	56-60	5	19
β-strand	64	1	64
β-strand	88	1	64
α-helix	89-91	3
β-strand	95-99	5	19
β-strand	100-103	4	63
β-strand	106	1	65
β-strand	112	1	65
β-strand	113-118	6	63
β-strand	121-126	6	63
β-strand	140-145	6	19

7 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
DNA-directed RNA polymerase II subunit RPB1	A	protein	1733	Saccharomyces cerevisiae S288C	P04050 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2	B	protein	1259	Saccharomyces cerevisiae S288C	P08518 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae S288C	P16370 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae S288C	P20434 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	155	Saccharomyces cerevisiae S288C	P20435
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	146	Saccharomyces cerevisiae S288C	P20436
DNA-directed RNA polymerase II subunit RPB9	I	protein	122	Saccharomyces cerevisiae S288C	P27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	70	Saccharomyces cerevisiae S288C	P22139
DNA-directed RNA polymerase II subunit RPB11	K	protein	120	Saccharomyces cerevisiae S288C	P38902
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	70	Saccharomyces cerevisiae S288C	P40422
DNA (38-mer)	N	DNA	48	synthetic construct
RNA	P	RNA	20	synthetic construct

6 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>8K5P_1 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 2 (B), FASTA

>8K5P_2 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
KLLFQELMAMNITPRLYTDRSRDFENLYFQGHHHHHHDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 3 (C), FASTA

>8K5P_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (E), FASTA

>8K5P_4 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 5 (F), FASTA

>8K5P_5 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 6 (H), FASTA

>8K5P_6 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 7 (I), FASTA

>8K5P_7 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 8 (J), FASTA

>8K5P_8 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 9 (K), FASTA

>8K5P_9 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 10 (L), FASTA

>8K5P_10 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Sequence of entity 11 (N), FASTA

>8K5P_11 DNA (38-MER) (chains N)
GCGTGTCTAGCACAGGATCGAGAGGTAATTCTGCTTATCGGTAGAGTG

Sequence of entity 12 (P), FASTA

>8K5P_12 RNA (chains P)
ACAGAUGUCCUCGAGAGGUA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	3

Primary citation

Structural basis of exoribonuclease-mediated mRNA transcription termination. Zeng, Y., Zhang, H.W., Wu, X.X. et al. Nature (2024) 628:887-893. DOI 10.1038/s41586-024-07240-3 · 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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