7ML2: RNA polymerase II pre-initiation complex

Name: PDB 7ML2: RNA polymerase II pre-initiation complex (PIC3)
Published: 2022-02-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RNA polymerase II pre-initiation complex (PIC3). Determined by electron microscopy at 3.4 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Saccharomyces cerevisiae
Chains: 30
Atoms: 64,550
Mol. weight: 1320.46 kDa
Ligands: SF4, MG, ZN
Released: 2 Feb 2022

Explore 7ML2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ML2 contains 363 α-helices and 379 β-strands across 28 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: 40 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	112
β-strand	9-11	3	112
α-helix	19-33	15
β-strand	39-41	3	113
α-helix	48-62	15
β-strand	69-73	5	113
α-helix	76-97	22
β-strand	105-108	4	113
α-helix	118-122	5
α-helix	126-136	11
α-helix	141-146	6
α-helix	158-161	4
α-helix	162-166	5
α-helix	178-187	10
α-helix	192-198	7
β-strand	205-208	4	113
α-helix	210-214	5
α-helix	224-227	4
β-strand	231-235	5	113
α-helix	240-248	9
β-strand	250	1	114
β-strand	253	1	114
α-helix	254-278	25
α-helix	280-290	11
α-helix	323-326	4
α-helix	328-346	19
β-strand	352	1	114
α-helix	356-366	11
α-helix	371-375	5
α-helix	377-388	12
α-helix	394-396	3
α-helix	397-411	15
β-strand	416-421	6	114
α-helix	425-427	3
β-strand	434-439	6	114
α-helix	443-452	10
β-strand	456-460	5	113
α-helix	468-473	6
β-strand	493-496	4	115
β-strand	499	1	116
β-strand	505	1	116
α-helix	516-532	17
β-strand	537-541	5	115
α-helix	544-556	13
α-helix	559-566	8
β-strand	568-571	4	115
α-helix	576-591	16
β-strand	596-601	6	115
α-helix	606-609	4
β-strand	619-620	2	115
β-strand	623	1	117
α-helix	634-644	11
α-helix	650-666	17
α-helix	667-669	3
β-strand	678-681	4	115
β-strand	682	1	117
α-helix	684-687	4
α-helix	695-700	6
α-helix	703-705	3
α-helix	710-725	16
α-helix	734-737	4
α-helix	745-749	5
α-helix	750-751	2

Chain 1: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	171-175	5
α-helix	178-187	10
α-helix	189-196	8
α-helix	206-212	7
α-helix	214-224	11
α-helix	231-236	6
α-helix	252-262	11
α-helix	264-272	9
α-helix	280-287	8
α-helix	288-292	5
α-helix	309-327	19
α-helix	372-387	16
α-helix	468-482	15
α-helix	497-515	19
α-helix	541-564	24
α-helix	576-603	28
α-helix	607-615	9
α-helix	617-638	22

Chain 2: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	11-16	6
α-helix	19-25	7
α-helix	29-35	7
α-helix	41-52	12
β-strand	57-58	2	31
α-helix	59-65	7
α-helix	71-83	13
β-strand	87	1	32
β-strand	97-98	2	31
β-strand	100	1	32
α-helix	102-112	11
α-helix	120-122	3
β-strand	124	1	33
α-helix	136-151	16
α-helix	161-169	9
α-helix	186-191	6
α-helix	197-210	14
α-helix	218-230	13
β-strand	234-235	2	33
α-helix	244-255	12
α-helix	261-262	2
α-helix	273-280	8
α-helix	354-361	8
β-strand	369	1	34
β-strand	374	1	34
α-helix	380-387	8
α-helix	395-402	8
α-helix	405-416	12
α-helix	422-425	4
α-helix	435-447	13
β-strand	454	1	35
β-strand	457-458	2	36
α-helix	465-478	14
β-strand	492-493	2	36
α-helix	496-506	11

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	29	1
β-strand	30	1	78
α-helix	31	1
α-helix	40-49	10
β-strand	52-53	2	79
β-strand	62-63	2	79
β-strand	69	1	78
α-helix	77-91	15
α-helix	104-122	19
α-helix	128-144	17

Chain 4: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	109
α-helix	36-42	7
α-helix	50-67	18
β-strand	73-78	6	109
β-strand	83-85	3	109
α-helix	117-134	18
α-helix	138-142	5
α-helix	149-166	18
β-strand	176-182	7	109
α-helix	193-205	13
β-strand	210-216	7	109
α-helix	222-230	9
β-strand	235-236	2	109
α-helix	245-251	7
β-strand	275	1	110
β-strand	282	1	110
α-helix	283	1
β-strand	287-288	2	111
β-strand	295-296	2	111
α-helix	311-313	3
α-helix	314-320	7

Chain 5: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	36
β-strand	8-11	4	35
α-helix	14-26	13
β-strand	31-36	6	35
β-strand	39-42	4	35
α-helix	44-61	18

Chain 6: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	125-129	5	118
α-helix	134-137	4
α-helix	145-163	19
β-strand	168-175	8	118
β-strand	178-186	9	118
α-helix	189-201	13
α-helix	210-220	11
α-helix	229	1
β-strand	230-234	5	118
α-helix	248-256	9
β-strand	259-263	5	118
α-helix	271-280	10
α-helix	294-302	9
β-strand	320	1	111
β-strand	323	1	119
β-strand	326-327	2	120
β-strand	347-348	2	120
β-strand	355-356	2	120
α-helix	362-363	2
β-strand	370	1	119
α-helix	374-383	10
β-strand	390-391	2	121
α-helix	419-422	4
β-strand	427-428	2	121
α-helix	438-444	7
α-helix	452-455	4

Chain 7: 32 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	66
α-helix	105-108	4
α-helix	122-124	3
α-helix	125-127	3
β-strand	132	1	67
β-strand	133-134	2	68
β-strand	141-142	2	68
α-helix	150-160	11
β-strand	162	1	69
β-strand	174	1	69
α-helix	177-184	8
α-helix	190-200	11
β-strand	201	1	67
α-helix	204-206	3
α-helix	207-218	12
β-strand	233	1	70
α-helix	239-246	8
β-strand	255	1	71
α-helix	263-267	5
β-strand	317	1	70
β-strand	318	1	71
α-helix	323-332	10
β-strand	353	1	72
α-helix	364-374	11
β-strand	383-384	2	73
α-helix	392-403	12
β-strand	407-411	5	73
α-helix	414-420	7
α-helix	421-425	5
β-strand	451	1	72
β-strand	453-456	4	73
α-helix	457-460	4
α-helix	468-479	12
β-strand	484-488	5	73
α-helix	495-498	4
β-strand	511-513	3	73
β-strand	523	1	66
α-helix	528-531	4
β-strand	534-536	3	73
α-helix	544-546	3
β-strand	553-555	3	74
β-strand	557-559	3	75
α-helix	560-561	2
α-helix	563-571	9
α-helix	575-577	3
α-helix	578-582	5
α-helix	585-600	16
β-strand	606-608	3	74
α-helix	613-622	10
α-helix	633-640	8
α-helix	641-645	5
β-strand	652-654	3	74
α-helix	664-666	3
β-strand	669-672	4	74
α-helix	680-690	11
β-strand	704-707	4	74
β-strand	708-710	3	75
α-helix	716-729	14
β-strand	732-734	3	74
α-helix	753-764	12

20 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

18 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7ML2_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

>7ML2_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

>7ML2_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (D), FASTA

>7ML2_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 5 (E), FASTA

>7ML2_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 6 (F), FASTA

>7ML2_6 DNA-directed RNA polymerases I,II,and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 7 (G), FASTA

>7ML2_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 8 (H), FASTA

>7ML2_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 9 (I), FASTA

>7ML2_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 10 (J), FASTA

>7ML2_10 DNA-directed RNA polymerases II subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 11 (K), FASTA

>7ML2_11 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 12 (L), FASTA

>7ML2_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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