6BM4: DNA-directed RNA polymerase II subunit RPB1

Name: PDB 6BM4: Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP
Published: 2018-02-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP. Determined by X-ray diffraction at 2.95 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
Chains: 12
Atoms: 28,274
Mol. weight: 482.38 kDa
Ligands: ZN, MG, 2KH
Released: 28 Feb 2018

Explore 6BM4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BM4 contains 167 α-helices and 203 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: 69 helices, 66 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	82-90	9	4
α-helix	93-95	3
α-helix	96-102	7
β-strand	106	1	5
β-strand	113	1	5
α-helix	122-125	4
α-helix	131-140	10
β-strand	176-177	2	6
β-strand	180-181	2	6
β-strand	202	1	6
α-helix	204-211	8
α-helix	220-222	3
α-helix	231-233	3
β-strand	236-241	6	4
α-helix	261-281	21
α-helix	289-304	16
α-helix	325-329	5
α-helix	335-339	5
β-strand	343-345	3	7
β-strand	348-355	8	8
β-strand	363-367	5	8
α-helix	368-373	6
β-strand	375-379	5	9
α-helix	385-394	10
β-strand	402-406	5	9
β-strand	412-414	3	9
β-strand	431-435	5	9
α-helix	436	1
β-strand	441-445	5	8
α-helix	452-454	3
β-strand	455-463	9	8
β-strand	468-470	3	8
α-helix	472-474	3
α-helix	475-478	4
β-strand	486-490	5	8
α-helix	495-504	10
β-strand	506	1	8
α-helix	508-510	3
β-strand	512-513	2	10
β-strand	518-519	2	10
α-helix	525-534	10
β-strand	540-541	2	11
α-helix	543-552	10
α-helix	559-563	5
β-strand	565-567	3	12
β-strand	571	1	12
β-strand	572-573	2	11
α-helix	574-578	5
α-helix	583	1
β-strand	588-590	3	13
β-strand	605-608	4	13
β-strand	611-614	4	13
α-helix	619-622	4
α-helix	629-637	9
α-helix	639-658	20
β-strand	663	1	14
α-helix	666-669	4
α-helix	673-698	26
α-helix	703-705	3
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	15
β-strand	769-770	2	16
β-strand	773-774	2	16
α-helix	775-776	2
β-strand	779	1	17
β-strand	782	1	17
α-helix	788	1
β-strand	799-800	2	15
α-helix	810-845	36
β-strand	849-850	2	18
β-strand	856-857	2	18
β-strand	863-865	3	18
α-helix	868-870	3
β-strand	873	1	19
α-helix	875-877	3
β-strand	878-882	5	20
α-helix	890-897	8
β-strand	913	1	21
α-helix	923-946	24
β-strand	953-957	5	20
α-helix	960-970	11
β-strand	979	1	21
α-helix	983-993	11
α-helix	1005-1014	10
α-helix	1016-1025	10
α-helix	1028-1029	2
α-helix	1030-1035	6
α-helix	1039-1056	18
β-strand	1057	1	19
α-helix	1058-1059	2
α-helix	1064-1073	10
α-helix	1098-1106	9
β-strand	1115	1	22
β-strand	1116-1117	2	23
β-strand	1118-1119	2	22
β-strand	1120	1	24
α-helix	1121	1
α-helix	1128-1138	11
β-strand	1141-1142	2	25
α-helix	1144-1146	3
β-strand	1147-1154	8	26
α-helix	1167-1172	6
β-strand	1191-1197	7	26
α-helix	1201-1204	4
α-helix	1209-1220	12
β-strand	1224-1228	5	26
β-strand	1237-1242	6	26
α-helix	1257-1268	12
β-strand	1272-1274	3	25
β-strand	1281-1287	7	22
β-strand	1290-1292	3	27
β-strand	1298-1300	3	27
β-strand	1303-1309	7	22
α-helix	1313-1316	4
β-strand	1322	1	24
β-strand	1328-1329	2	23
α-helix	1332-1338	7
α-helix	1341-1358	18
α-helix	1365-1376	12
α-helix	1389-1391	3
α-helix	1396-1400	5
α-helix	1406-1415	10
α-helix	1417	1
β-strand	1418-1419	2	2
α-helix	1424-1430	7
α-helix	1437-1439	3
β-strand	1441-1445	5	28

Chain B: 55 helices, 79 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	29
α-helix	25	1
α-helix	30-39	10
α-helix	45-53	9
α-helix	54-58	5
α-helix	59-64	6
β-strand	68-69	2	30
β-strand	90-91	2	30
β-strand	92-97	6	31
β-strand	101-103	3	32
β-strand	109-111	3	32
α-helix	114-119	6
β-strand	125-132	8	31
β-strand	165-171	7	31
α-helix	172-173	2
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
α-helix	228-229	2
β-strand	234-242	9	35
β-strand	252-259	8	35
β-strand	262	1	36
β-strand	264	1	36
β-strand	269-272	4	35
β-strand	280-281	2	35
α-helix	282-288	7
α-helix	296-301	6
α-helix	308-320	13
α-helix	327-337	11
α-helix	347-354	8
α-helix	355-359	5
α-helix	372-389	18
α-helix	401-403	3
β-strand	404-407	4	34
α-helix	409-434	26
α-helix	451-463	13
β-strand	480-482	3	33
α-helix	488-495	8
β-strand	497-499	3	34
α-helix	516-518	3
β-strand	522	1	37
β-strand	537-538	2	34
β-strand	539	1	37
β-strand	544-545	2	38
α-helix	552-559	8
β-strand	564	1	39
α-helix	566-568	3
α-helix	571-573	3
α-helix	577	1
β-strand	578-582	5	39
β-strand	585-590	6	39
α-helix	593-606	14
β-strand	614-618	5	39
β-strand	623-627	5	39
β-strand	633-639	7	38
β-strand	640-641	2	40
β-strand	650-651	2	40
β-strand	654	1	29
α-helix	655-667	13
α-helix	681-686	6
β-strand	690-694	5	38
α-helix	695-698	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	759-761	3
α-helix	764-773	10
α-helix	774-776	3
β-strand	777	1	41
α-helix	783-787	5
β-strand	792-796	5	42
β-strand	800	1	43
β-strand	804-805	2	44
α-helix	809-811	3
β-strand	821-827	7	45
β-strand	828	1	14
β-strand	838-842	5	45
α-helix	843-847	5
β-strand	853-862	10	42
β-strand	865	1	46
β-strand	871	1	46
β-strand	873-874	2	47
β-strand	882-883	2	47
β-strand	893	1	48
β-strand	898	1	49
β-strand	899	1	48
α-helix	900	1
β-strand	904-906	3	42
β-strand	910-912	3	49
β-strand	914-916	3	47
β-strand	934-936	3	47
β-strand	939-940	2	49
α-helix	941-942	2
β-strand	946-956	11	42
β-strand	962-972	11	42
α-helix	973-974	2
β-strand	979-982	4	45
β-strand	987-994	8	45
β-strand	1001-1002	2	50
β-strand	1010-1012	3	45
α-helix	1014-1016	3
α-helix	1023-1038	16
β-strand	1042-1043	2	44
α-helix	1052-1061	10
β-strand	1069-1070	2	45
β-strand	1072-1073	2	50
α-helix	1079	1
β-strand	1080	1	50
α-helix	1081	1
β-strand	1085-1094	10	45
β-strand	1095	1	41
α-helix	1099-1101	3
β-strand	1104-1106	3	8
α-helix	1110	1
β-strand	1111	1	51
α-helix	1112	1
β-strand	1118	1	51
α-helix	1119	1
β-strand	1128-1130	3	7
α-helix	1132-1141	10
α-helix	1144-1150	7
β-strand	1157-1163	7	1
β-strand	1172-1174	3	52
β-strand	1179-1181	3	52
β-strand	1191-1197	7	1
α-helix	1198-1208	11
β-strand	1212	1	3
β-strand	1215-1217	3	2

Chain C: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	53
β-strand	17-23	7	53
α-helix	27-39	13
β-strand	43-54	12	54
α-helix	60-69	10
β-strand	72	1	55
α-helix	77-79	3
β-strand	96-104	9	54
β-strand	111-114	4	56
α-helix	115-117	3
β-strand	119-120	2	54
α-helix	131	1
β-strand	132	1	55
α-helix	133	1
β-strand	143-147	5	56
β-strand	152-162	11	54
α-helix	168-170	3
β-strand	173-180	8	53
α-helix	197-200	4
α-helix	202-204	3
α-helix	205-209	5
α-helix	211-214	4
β-strand	228-234	7	53
α-helix	240-264	25

Chain E: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
β-strand	28	1	57
α-helix	32-35	4
α-helix	39-46	8
β-strand	47	1	58
β-strand	53	1	58
α-helix	55-57	3
β-strand	61-62	2	59
β-strand	64	1	57
α-helix	66-71	6
β-strand	78-82	5	59
β-strand	87-88	2	60
α-helix	90-103	14
β-strand	107-112	6	59
β-strand	115-116	2	60
β-strand	131-136	6	59
α-helix	137-139	3
α-helix	144-146	3
α-helix	151	1
β-strand	152-155	4	61
α-helix	158-167	10
α-helix	172-174	3
β-strand	177-178	2	61
α-helix	183-188	6
α-helix	190-191	2
β-strand	195-202	8	61
β-strand	206-214	9	61

Chain F: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	84	1	62
α-helix	85-86	2
α-helix	87-101	15
α-helix	105-107	3
α-helix	117-126	10
β-strand	132-137	6	28
α-helix	138	1
β-strand	143-147	5	28
β-strand	152	1	62

Chain H: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-16	13	12
β-strand	23-30	8	12
β-strand	37-43	7	12
β-strand	54-60	7	12
β-strand	95-98	4	12
β-strand	100-106	7	12
β-strand	112-118	7	12
β-strand	121-127	7	12
β-strand	141-145	5	12

Chain I: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	63
α-helix	12	1
β-strand	13	1	63
α-helix	14	1
β-strand	15-19	5	64
β-strand	24-28	5	64
β-strand	35-37	3	64
β-strand	44-47	4	26
α-helix	60-64	5
α-helix	73-75	3
β-strand	83-87	5	65
β-strand	99-103	5	65
β-strand	109-111	3	65

Chain J: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	66
β-strand	13	1	66
α-helix	18-26	9
α-helix	32-38	7
α-helix	44-51	8
β-strand	53	1	43
α-helix	57-60	4

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
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
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	70	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40422
DNA (5'-D(PCPAP(3DR)PCPTPCPTPTPGPAPTPG)-3')	T	DNA	29	synthetic construct
RNA (5'-r(apupcpapapgpapgp*a)-3')	R	RNA	9	synthetic construct

Sequence of entity 1 (A), FASTA

>6BM4_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

>6BM4_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
KLLFQELMAMNITPRLYTDRSRDF

Sequence of entity 3 (C), FASTA

>6BM4_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (E), FASTA

>6BM4_4 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 5 (F), FASTA

>6BM4_5 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 6 (H), FASTA

>6BM4_6 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 7 (I), FASTA

>6BM4_7 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 8 (J), FASTA

>6BM4_8 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 9 (K), FASTA

>6BM4_9 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 10 (L), FASTA

>6BM4_10 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Sequence of entity 11 (T), FASTA

>6BM4_11 DNA (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3') (chains T)
CTACCGATAAGCAGAGGCANCTCTCGATG

Sequence of entity 12 (R), FASTA

>6BM4_12 RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3') (chains R)
AUCGAGAGA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
MG	Magnesium ion	Mg	2
2KH	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine	C9 H16 N3 O14 P3	1

Primary citation

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Wang, W., Walmacq, C., Chong, J. et al. Proc Natl Acad Sci U S A (2018) 115:E2538-E2545. DOI 10.1073/pnas.1722050115 · 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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