7ML0: RNA polymerase II pre-initiation complex

Name: PDB 7ML0: RNA polymerase II pre-initiation complex (PIC1)
Published: 2022-02-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RNA polymerase II pre-initiation complex (PIC1). Determined by electron microscopy at 3.0 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae
Chains: 28
Atoms: 64,214
Mol. weight: 1280.88 kDa
Ligands: SF4, MG, ZN
Released: 2 Feb 2022

Explore 7ML0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ML0 contains 380 α-helices and 383 β-strands across 26 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 0: 39 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	100
β-strand	9-11	3	100
α-helix	19-33	15
β-strand	36	1	101
β-strand	40-41	2	102
α-helix	48-62	15
β-strand	69-73	5	103
α-helix	76-96	21
β-strand	105-106	2	103
α-helix	118-122	5
α-helix	126-136	11
α-helix	139-146	8
α-helix	158-161	4
α-helix	162-166	5
β-strand	167	1	104
β-strand	169	1	104
α-helix	178-187	10
α-helix	192-199	8
β-strand	205-209	5	103
α-helix	210-214	5
α-helix	224-227	4
β-strand	231-235	5	103
α-helix	237-239	3
α-helix	240-244	5
β-strand	250	1	105
β-strand	253	1	105
α-helix	254-277	24
α-helix	280-290	11
α-helix	295-298	4
α-helix	323-326	4
α-helix	328-346	19
β-strand	352-354	3	105
α-helix	356-366	11
α-helix	371-386	16
α-helix	394-411	18
β-strand	416-421	6	105
α-helix	425-427	3
β-strand	434-439	6	105
α-helix	442-452	11
β-strand	455	1	101
β-strand	456-459	4	103
α-helix	468-473	6
β-strand	481-482	2	102
α-helix	484-486	3
β-strand	493-494	2	106
β-strand	497	1	106
β-strand	499	1	107
β-strand	505	1	107
α-helix	516-532	17
β-strand	537-541	5	106
α-helix	544-556	13
α-helix	559-566	8
β-strand	569-570	2	106
α-helix	576-591	16
β-strand	597-601	5	106
α-helix	605-609	5
β-strand	619-623	5	106
α-helix	633-645	13
α-helix	650-666	17
α-helix	667-669	3
β-strand	678-682	5	106
α-helix	684-692	9
α-helix	695-700	6
β-strand	708	1	106
α-helix	710-725	16
α-helix	734-738	5
α-helix	744-751	8

Chain 1: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	171-174	4
α-helix	178-185	8
α-helix	189-199	11
α-helix	206-210	5
α-helix	214-224	11
α-helix	227-229	3
α-helix	231-234	4
α-helix	252-262	11
α-helix	264-272	9
α-helix	283-294	12
α-helix	309-311	3
α-helix	312-329	18
α-helix	339-344	6
α-helix	372-390	19
α-helix	469-482	14
α-helix	497-515	19
α-helix	541-566	26
α-helix	576-604	29
α-helix	607-615	9
α-helix	617-638	22

Chain 2: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
α-helix	19-25	7
α-helix	29-38	10
α-helix	41-51	11
β-strand	57	1	118
α-helix	60-63	4
α-helix	71-83	13
β-strand	87-90	4	118
β-strand	97-100	4	118
α-helix	102-112	11
α-helix	138-151	14
α-helix	161-170	10
α-helix	186-193	8
α-helix	197	1
α-helix	198-202	5
α-helix	203-210	8
α-helix	218-230	13
α-helix	244-256	13
β-strand	260	1	119
β-strand	270	1	119
α-helix	273-278	6
α-helix	356-361	6
β-strand	365-369	5	120
β-strand	374-377	4	120
α-helix	380-389	10
α-helix	394-402	9
α-helix	405-408	4
α-helix	411-414	4
α-helix	436-449	14
β-strand	452-453	2	121
β-strand	458-459	2	122
β-strand	483	1	123
α-helix	486-488	3
β-strand	491	1	122
β-strand	492	1	123

Chain 3: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	37
β-strand	30	1	38
β-strand	39	1	37
α-helix	40-47	8
β-strand	52-53	2	39
β-strand	62-63	2	39
α-helix	65-67	3
β-strand	69	1	38
α-helix	76-91	16
α-helix	92-94	3
α-helix	103-122	20
α-helix	128-142	15

Chain 4: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	108
α-helix	34-42	9
α-helix	50-67	18
β-strand	73-78	6	108
β-strand	83-85	3	108
α-helix	118-134	17
α-helix	138-142	5
α-helix	149-166	18
β-strand	175-182	8	108
α-helix	193-206	14
β-strand	212-216	5	108
α-helix	222-231	10
β-strand	235	1	108
α-helix	245-251	7
β-strand	276	1	109
β-strand	281	1	109
β-strand	287-288	2	110
β-strand	295	1	110
α-helix	314-319	6
α-helix	320-322	3

Chain 5: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	122
β-strand	8-11	4	121
α-helix	14-27	14
β-strand	33-36	4	121
β-strand	39-42	4	121
α-helix	47-61	15

Chain 6: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	124-131	8	111
α-helix	134-137	4
α-helix	145-163	19
β-strand	168-175	8	111
β-strand	178-186	9	111
α-helix	189-201	13
α-helix	210-220	11
β-strand	229-235	7	111
α-helix	248-256	9
β-strand	260	1	111
β-strand	263	1	111
β-strand	265	1	112
α-helix	271-280	10
β-strand	290	1	112
α-helix	294-305	12
β-strand	320-321	2	110
β-strand	323	1	113
β-strand	335	1	114
β-strand	343	1	114
β-strand	347-348	2	115
β-strand	355-356	2	115
β-strand	362	1	116
β-strand	369	1	116
β-strand	370	1	113
α-helix	374-380	7
α-helix	387-389	3
β-strand	390	1	117
α-helix	391	1
β-strand	428	1	117
α-helix	438-444	7
α-helix	452-455	4

Chain 7: 26 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	104	1	63
β-strand	112	1	64
α-helix	125-128	4
β-strand	132	1	65
β-strand	143	1	65
β-strand	144	1	66
β-strand	147	1	66
α-helix	151-153	3
α-helix	154-158	5
β-strand	175	1	64
α-helix	177-183	7
α-helix	190-199	10
α-helix	207-216	10
β-strand	227	1	67
β-strand	232	1	67
α-helix	242-244	3
α-helix	305-307	3
α-helix	326-332	7
α-helix	367-371	5
β-strand	382-385	4	68
α-helix	392-401	10
β-strand	407-409	3	68
β-strand	410	1	69
α-helix	417-419	3
β-strand	455	1	69
α-helix	457-460	4
α-helix	469-479	11
β-strand	484-488	5	68
α-helix	495-502	8
β-strand	510-514	5	68
β-strand	527	1	63
β-strand	534	1	68
β-strand	553-559	7	70
α-helix	563-569	7
α-helix	576-582	7
α-helix	585-600	16
β-strand	605-608	4	70
α-helix	612-622	11
α-helix	634-639	6
α-helix	658-660	3
β-strand	669-672	4	70
α-helix	680-686	7
α-helix	688-691	4
β-strand	705-710	6	70
α-helix	716-723	8
α-helix	727-729	3
β-strand	732-735	4	70
α-helix	753-769	17

18 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 subunit	A	protein	1733	Saccharomyces cerevisiae	P04050 (AlphaFold model)
DNA-directed RNA polymerase subunit beta	B	protein	1224	Saccharomyces cerevisiae	P08518 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae	P16370 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae	P20433 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae	P20434
DNA-directed RNA polymerases I,II,and III subunit RPABC2	F	protein	155	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	H	protein	146	Saccharomyces cerevisiae	P20436
DNA-directed RNA polymerase II subunit RPB9	I	protein	122	Saccharomyces cerevisiae	P27999
DNA-directed RNA polymerases II subunit RPABC5	J	protein	70	Saccharomyces cerevisiae	P22139
DNA-directed RNA polymerase II subunit RPB11	K	protein	120	Saccharomyces cerevisiae	P38902
DNA-directed RNA polymerases II subunit RPABC4	L	protein	70	Saccharomyces cerevisiae	P40422

16 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7ML0_1 DNA-directed RNA polymerase subunit (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

>7ML0_2 DNA-directed RNA polymerase subunit beta (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

>7ML0_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (D), FASTA

>7ML0_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 5 (E), FASTA

>7ML0_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 6 (F), FASTA

>7ML0_6 DNA-directed RNA polymerases I,II,and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 7 (G), FASTA

>7ML0_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 8 (H), FASTA

>7ML0_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 9 (I), FASTA

>7ML0_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 10 (J), FASTA

>7ML0_10 DNA-directed RNA polymerases II subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 11 (K), FASTA

>7ML0_11 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 12 (L), FASTA

>7ML0_12 DNA-directed RNA polymerases II subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	17

Primary citation

Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Yang, C., Fujiwara, R., Kim, H.J. et al. Mol Cell (2022) 82:660-676.e9. DOI 10.1016/j.molcel.2021.12.020 · 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…

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