5FMF: DNA repair helicase RAD25, SSL2

the P-lobe of RNA polymerase II pre-initiation complex. Determined by electron microscopy at 6.0 Å resolution. Released 25 Nov 2015.

Method: Electron microscopy
Resolution: 6.0 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 27
Atoms: 54,672
Mol. weight: 873.74 kDa
Ligands: MG, ZN
Released: 25 Nov 2015

Explore 5FMF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FMF contains 322 α-helices and 349 β-strands across 25 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 1: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	296-301	6	1
β-strand	304-308	5	1
β-strand	316-317	2	1
β-strand	322-326	5	1
α-helix	327-333	7
α-helix	334-339	6
β-strand	343-345	3	1
α-helix	350-352	3
α-helix	364-374	11
β-strand	382-385	4	2
α-helix	388-390	3
α-helix	392-403	12
β-strand	407-411	5	2
α-helix	414-423	10
α-helix	424-426	3
β-strand	436-437	2	2
β-strand	438	1	3
β-strand	443	1	3
β-strand	453-456	4	2
α-helix	466-469	4
β-strand	484-488	5	2
α-helix	490-492	3
α-helix	499-503	5
β-strand	509-514	6	2
α-helix	523-526	4
α-helix	527-530	4
β-strand	534-537	4	2
β-strand	552-559	8	4
α-helix	560-562	3
α-helix	563-571	9
α-helix	575-577	3
α-helix	578-583	6
α-helix	585-599	15
β-strand	605-608	4	4
α-helix	612-621	10
β-strand	626-627	2	4
α-helix	633-645	13
β-strand	651-654	4	4
α-helix	656-658	3
α-helix	664-666	3
β-strand	667	1	5
β-strand	669-672	4	4
α-helix	680-690	11
β-strand	691	1	5
β-strand	703-710	8	4
α-helix	714-716	3
α-helix	717-728	12
β-strand	732-736	5	4
α-helix	753-771	19
α-helix	774-779	6
α-helix	781-783	3

Chain 2: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	242-254	13
β-strand	279-282	4	11
β-strand	296-299	4	11
β-strand	305-307	3	11

Chain A: 78 helices, 74 β-strands

Element	Residues	Length	Sheet
α-helix	10	1
β-strand	11-12	2	12
β-strand	16-18	3	13
β-strand	21	1	14
α-helix	24-30	7
β-strand	41	1	15
β-strand	49	1	15
β-strand	82-91	10	16
α-helix	96-105	10
β-strand	106	1	17
β-strand	113	1	17
α-helix	120-127	8
α-helix	131-142	12
β-strand	147	1	18
β-strand	151-153	3	19
β-strand	161-163	3	19
β-strand	170	1	18
α-helix	171	1
β-strand	172-176	5	20
β-strand	181-185	5	20
β-strand	198-202	5	20
α-helix	203	1
α-helix	204-213	10
α-helix	216-221	6
β-strand	225	1	21
β-strand	229	1	21
α-helix	231-234	4
β-strand	235-241	7	16
α-helix	242-243	2
α-helix	244-246	3
β-strand	250-251	2	22
β-strand	257-258	2	22
α-helix	261-281	21
α-helix	286-288	3
α-helix	289-304	16
α-helix	312-314	3
β-strand	315-316	2	23
β-strand	320-321	2	23
α-helix	322	1
α-helix	325-329	5
α-helix	335-339	5
β-strand	343-345	3	24
β-strand	348-356	9	25
β-strand	363-367	5	25
α-helix	368-373	6
β-strand	375-379	5	26
α-helix	385-394	10
β-strand	402-406	5	26
α-helix	411	1
β-strand	412-414	3	26
β-strand	431-435	5	26
α-helix	436	1
β-strand	441-445	5	25
α-helix	452-454	3
β-strand	455-463	9	25
β-strand	468-471	4	25
α-helix	472-474	3
α-helix	475-478	4
β-strand	486-490	5	25
α-helix	495-504	10
β-strand	506	1	25
α-helix	507-510	4
β-strand	512-513	2	27
β-strand	518-519	2	27
α-helix	525-534	10
β-strand	540-542	3	28
α-helix	543-551	9
α-helix	561-563	3
β-strand	565	1	28
β-strand	571-573	3	28
α-helix	574-578	5
β-strand	588-590	3	29
β-strand	605-607	3	29
β-strand	612-614	3	29
α-helix	619-622	4
α-helix	629-637	9
α-helix	639-660	22
β-strand	663	1	30
α-helix	666-668	3
α-helix	673-698	26
α-helix	704-705	2
α-helix	710-736	27
α-helix	742-749	8
α-helix	755-762	8
β-strand	766-767	2	31
β-strand	769-770	2	32
β-strand	773-774	2	32
α-helix	776	1
β-strand	779	1	33
β-strand	782	1	33
β-strand	799-800	2	31
α-helix	810-845	36
β-strand	849-850	2	34
β-strand	856-857	2	34
β-strand	863-865	3	34
α-helix	868-870	3
β-strand	873	1	35
α-helix	875-877	3
β-strand	878-882	5	36
α-helix	890-897	8
α-helix	908-909	2
β-strand	913	1	37
α-helix	916-919	4
α-helix	923-946	24
β-strand	953-957	5	36
α-helix	960-971	12
α-helix	978	1
β-strand	979	1	37
α-helix	983-995	13
α-helix	1005-1025	21
α-helix	1028-1029	2
α-helix	1030-1034	5
α-helix	1039-1056	18
β-strand	1057	1	35
α-helix	1058-1059	2
α-helix	1064-1077	14
α-helix	1098-1105	8
β-strand	1116-1119	4	38
β-strand	1120	1	39
α-helix	1121	1
α-helix	1128-1138	11
β-strand	1142	1	40
α-helix	1143-1146	4
β-strand	1147-1154	8	41
α-helix	1167-1172	6
β-strand	1191-1197	7	41
α-helix	1199-1204	6
α-helix	1209-1220	12
α-helix	1221-1223	3
β-strand	1224-1228	5	41
β-strand	1236-1242	7	41
α-helix	1257-1270	14
β-strand	1272	1	40
β-strand	1280-1287	8	38
β-strand	1290-1292	3	42
β-strand	1298-1300	3	42
β-strand	1303-1309	7	38
α-helix	1313-1317	5
β-strand	1322	1	39
β-strand	1328-1329	2	38
α-helix	1332-1339	8
α-helix	1341-1358	18
α-helix	1365-1376	12
α-helix	1389-1391	3
α-helix	1396-1399	4
α-helix	1400-1404	5
α-helix	1405-1414	10
β-strand	1418-1419	2	13
α-helix	1424-1429	6
α-helix	1437-1439	3
β-strand	1442-1445	4	43
α-helix	1447-1452	6

Chain B: 58 helices, 83 β-strands

Element	Residues	Length	Sheet
α-helix	23	1
β-strand	24	1	44
α-helix	25	1
α-helix	30-41	12
α-helix	45-53	9
α-helix	54-58	5
α-helix	59-64	6
β-strand	69-74	6	45
β-strand	85-90	6	45
β-strand	91-100	10	46
β-strand	101-103	3	47
β-strand	109-111	3	47
α-helix	114-119	6
β-strand	125-133	9	46
β-strand	136-139	4	45
β-strand	164-171	8	46
α-helix	172	1
β-strand	173	1	48
α-helix	180-183	4
α-helix	186-191	6
β-strand	203-205	3	48
β-strand	208-212	5	48
α-helix	213	1
β-strand	214-218	5	49
β-strand	223-227	5	50
β-strand	234-241	8	50
β-strand	253-260	8	50
β-strand	269-272	4	50
β-strand	279-281	3	50
α-helix	282-289	8
α-helix	296-301	6
α-helix	308-312	5
α-helix	315-320	6
α-helix	327-336	10
α-helix	345-350	6
α-helix	353-358	6
α-helix	371-389	19
α-helix	394-396	3
α-helix	401-403	3
β-strand	404-407	4	49
α-helix	409-437	29
α-helix	444-447	4
α-helix	451-463	13
β-strand	480-482	3	48
α-helix	483-484	2
α-helix	488-494	7
β-strand	497-499	3	49
α-helix	516-518	3
β-strand	522	1	51
β-strand	536-538	3	49
β-strand	539	1	51
β-strand	540	1	52
β-strand	544-545	2	53
α-helix	552-559	8
β-strand	563-565	3	54
α-helix	566-568	3
α-helix	577	1
β-strand	578-582	5	54
β-strand	586-590	5	54
α-helix	593-606	14
β-strand	614-618	5	54
β-strand	623-627	5	54
β-strand	633-639	7	53
β-strand	640-641	2	55
β-strand	650-651	2	55
β-strand	654	1	44
α-helix	655-666	12
α-helix	681-686	6
β-strand	690-694	5	53
α-helix	695-698	4
β-strand	703-704	2	53
α-helix	708-710	3
α-helix	713-714	2
α-helix	728-729	2
β-strand	740-741	2	53
α-helix	745-748	4
β-strand	750	1	52
α-helix	753-755	3
α-helix	759-761	3
β-strand	762	1	56
α-helix	764-773	10
α-helix	774-776	3
β-strand	777	1	57
α-helix	785-787	3
β-strand	793-796	4	58
β-strand	800	1	59
β-strand	804-805	2	60
α-helix	807-810	4
β-strand	820-827	8	61
β-strand	828	1	30
β-strand	838-842	5	61
α-helix	843-847	5
β-strand	853-862	10	58
β-strand	865-866	2	62
β-strand	870-871	2	62
β-strand	873-874	2	63
β-strand	882-883	2	63
β-strand	898	1	64
α-helix	899-900	2
β-strand	901	1	65
β-strand	903	1	65
β-strand	904	1	58
β-strand	910-912	3	64
β-strand	914-917	4	63
β-strand	934-936	3	63
β-strand	939-940	2	64
α-helix	941-942	2
β-strand	948-956	9	58
β-strand	962-972	11	58
β-strand	979-981	3	61
β-strand	987-994	8	61
β-strand	1001-1002	2	61
β-strand	1010-1012	3	61
α-helix	1017-1020	4
β-strand	1022	1	56
α-helix	1023-1038	16
β-strand	1042-1043	2	60
α-helix	1052-1061	10
β-strand	1069-1073	5	61
α-helix	1079	1
β-strand	1080-1094	15	61
β-strand	1095	1	57
α-helix	1099-1101	3
β-strand	1104-1106	3	25
β-strand	1111	1	66
β-strand	1118	1	66
α-helix	1119-1120	2
α-helix	1121-1124	4
α-helix	1126-1127	2
β-strand	1128-1130	3	24
α-helix	1132-1141	10
α-helix	1144-1151	8
β-strand	1157-1163	7	12
β-strand	1174	1	67
β-strand	1179	1	67
β-strand	1182	1	68
β-strand	1187	1	68
β-strand	1191-1197	7	12
α-helix	1198-1209	12
β-strand	1212	1	14
β-strand	1215-1217	3	13

Chain C: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	69
β-strand	17-23	7	69
α-helix	27-39	13
β-strand	43-54	12	70
α-helix	60-69	10
β-strand	72-74	3	71
α-helix	76-79	4
α-helix	81-82	2
β-strand	96-104	9	70
α-helix	110	1
β-strand	111-114	4	72
α-helix	115-117	3
β-strand	119-120	2	70
β-strand	129-132	4	71
α-helix	133	1
β-strand	143-147	5	72
β-strand	152-162	11	70
α-helix	168-170	3
β-strand	173-179	7	69
α-helix	197-200	4
α-helix	202-204	3
α-helix	205-209	5
β-strand	228-234	7	69
α-helix	240-265	26

Chain D: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	73
β-strand	24	1	74
β-strand	28	1	74
β-strand	36-38	3	75
β-strand	44-46	3	75
β-strand	48-49	2	73
α-helix	54-72	19
α-helix	120-133	14
α-helix	139-151	13
α-helix	157-167	11
α-helix	174-182	9
α-helix	188-194	7
α-helix	196-198	3
α-helix	204-215	12

Chain E: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-27	22
β-strand	28	1	76
α-helix	32-35	4
α-helix	39-46	8
β-strand	47	1	77
β-strand	53	1	77
α-helix	55-58	4
β-strand	60-62	3	78
β-strand	64	1	76
α-helix	66-71	6
β-strand	78-82	5	78
β-strand	87-88	2	79
α-helix	90-102	13
β-strand	107-112	6	78
β-strand	115-116	2	79
α-helix	118-121	4
β-strand	131-136	6	78
α-helix	137-140	4
α-helix	144-146	3
β-strand	152-155	4	80
α-helix	156-157	2
α-helix	158-168	11
α-helix	172-174	3
β-strand	177-178	2	80
α-helix	183-187	5
β-strand	195-202	8	80
β-strand	206-214	9	80

Chain F: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	76-78	3
β-strand	84	1	81
α-helix	85-86	2
α-helix	87-102	16
α-helix	105-107	3
α-helix	117-126	10
β-strand	132-137	6	43
β-strand	143-147	5	43
β-strand	152	1	81

17 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 repair helicase RAD25, SSL2	1	protein	492	SACCHAROMYCES CEREVISIAE	Q00578 (AlphaFold model)
Transcription elongation factor S-II, DST1	2	protein	174	SACCHAROMYCES CEREVISIAE	P07273 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB1	A	protein	1733	SACCHAROMYCES CEREVISIAE	P04050 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2	B	protein	1224	SACCHAROMYCES CEREVISIAE	P08518 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	266	SACCHAROMYCES CEREVISIAE	P16370
RNA polymerase II pre-initiation complex, RPB4	D	protein	178	SACCHAROMYCES CEREVISIAE	P20433
DNA-directed RNA polymerases I, II, and III subunit RPABC1, RPB5	E	protein	214	SACCHAROMYCES CEREVISIAE	P20434
DNA-directed RNA polymerases I, II, and III subunit RPABC2, RPB6	F	protein	84	SACCHAROMYCES CEREVISIAE	P20435
DNA-directed RNA polymerase II subunit RPB7	G	protein	171	SACCHAROMYCES CEREVISIAE	P34087
DNA-directed RNA polymerases I, II, and III subunit RPABC3, RPB8	H	protein	146	SACCHAROMYCES CEREVISIAE	P20436
DNA-directed RNA polymerase II subunit RPB9	I	protein	119	SACCHAROMYCES CEREVISIAE	P27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5, RPB10	J	protein	65	SACCHAROMYCES CEREVISIAE	P22139

15 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>5FMF_1 DNA REPAIR HELICASE RAD25, SSL2 (chains 1)
SAVIGGDNEREEEDDDIDAVHSFEIANESVEVVKKRCQEIDYPVLEEYDFRNDHRNPDLD
IDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTS
SVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESGLVVSTYSMVANTRNRSHDSQKV
MDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGP
KLYEANWMELSQKGHIANVQCAEVWCPMTAEFYQEYLRETARKRMLLYIMNPTKFQACQF
LIQYHERRGDKIIVFSDNVYALQEYALKMGKPFIYGSTPQQERMNILQNFQYNDQINTIF
LSKVGDTSIDLPEATCLIQISSHYGSRRQEAQRLGRILRAKRRNDEGFNAFFYSLVSKDT
QEMYYSTKRQAFLVDQGYAFKVITHLHGMENIPNLAYASPRERRELLQEVLLKNEEAAGI
EVGDDADNSVGR

Sequence of entity 2 (2), FASTA

>5FMF_2 TRANSCRIPTION ELONGATION FACTOR S-II, DST1 (chains 2)
NDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAAY
KARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYN
AQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKFS

Sequence of entity 3 (A), FASTA

>5FMF_3 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 4 (B), FASTA

>5FMF_4 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 5 (C), FASTA

>5FMF_5 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 (chains C)
EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEF
IAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS
NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDP
WNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ
VVVRGIDTLQKKVASILLALTQMDQD

Sequence of entity 6 (D), FASTA

>5FMF_6 RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4 (chains D)
VSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEA
LVERRRAFKRSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAV
IQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 7 (E), FASTA

>5FMF_7 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5 (chains E)
DQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQ
ANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAM
KLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRA
DPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 8 (F), FASTA

>5FMF_8 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6 (chains F)
KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIP
LVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 9 (G), FASTA

>5FMF_9 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 10 (H), FASTA

>5FMF_10 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 11 (I), FASTA

>5FMF_11 DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 (chains I)
TTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQD
IGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ

Sequence of entity 12 (J), FASTA

>5FMF_12 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	9

Primary citation

Structure of an RNA Polymerase II Pre-Initiation Complex. Murakami, K., Tsai, K., Kalisman, N. et al. Proc Natl Acad Sci U S A (2015) 112:13543. DOI 10.1073/PNAS.1518255112 · PubMed

Other PDB entries of the same protein (UniProt Q00578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O4J 2.9 Å, Yeast RNA polymerase II transcription pre-initiation complex (consensus)
7ML0 3.0 Å, RNA polymerase II pre-initiation complex (PIC1)
8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
7ML4 3.1 Å, RNA polymerase II initially transcribing complex (ITC)
7ZS9 3.1 Å, Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome…
7O4I 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with initial transcription…
7O75 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
7ML2 3.4 Å, RNA polymerase II pre-initiation complex (PIC3)
7O4L 3.4 Å, Yeast TFIIH in the expanded state within the pre-initiation complex
7O72 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA
7O73 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed distorted…
7O4K 3.6 Å, Yeast TFIIH in the contracted state within the pre-initiation complex

Browse structure collections

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