7ML4: RNA polymerase II initially transcribing complex

Name: PDB 7ML4: RNA polymerase II initially transcribing complex (ITC)
Published: 2022-02-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

RNA polymerase II initially transcribing complex (ITC). Determined by electron microscopy at 3.1 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae
Chains: 31
Atoms: 62,733
Mol. weight: 1333.46 kDa
Ligands: SF4, MG, ZN
Released: 2 Feb 2022

Explore 7ML4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ML4 contains 362 α-helices and 375 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: 41 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	94
β-strand	9-11	3	94
α-helix	19-33	15
β-strand	40-41	2	95
α-helix	48-62	15
β-strand	69-73	5	95
α-helix	76-97	22
β-strand	107-108	2	95
α-helix	118-121	4
α-helix	126-136	11
α-helix	143-146	4
α-helix	159-161	3
α-helix	162-166	5
α-helix	178-187	10
α-helix	192-198	7
α-helix	199-201	3
β-strand	206-209	4	95
α-helix	211-214	4
α-helix	224-226	3
β-strand	231-235	5	95
α-helix	237-239	3
α-helix	241-247	7
β-strand	250	1	96
α-helix	254-277	24
α-helix	279-284	6
α-helix	287-291	5
α-helix	295-298	4
α-helix	328-344	17
β-strand	354	1	96
α-helix	356-366	11
α-helix	371-374	4
α-helix	377-385	9
α-helix	386-388	3
α-helix	397-409	13
β-strand	417-419	3	96
α-helix	425-427	3
β-strand	436-438	3	96
α-helix	443-452	10
β-strand	455-459	5	95
α-helix	468-473	6
β-strand	481-482	2	95
β-strand	492-494	3	97
β-strand	499	1	98
β-strand	505	1	98
α-helix	516-532	17
β-strand	537-541	5	99
α-helix	544-556	13
α-helix	559-566	8
β-strand	568-571	4	99
α-helix	576-591	16
β-strand	596-601	6	99
α-helix	606-609	4
β-strand	619-620	2	97
β-strand	621	1	99
β-strand	623	1	100
α-helix	634-645	12
α-helix	650-666	17
α-helix	667-669	3
β-strand	677-679	3	97
β-strand	682	1	100
α-helix	684-690	7
α-helix	695-700	6
α-helix	703-705	3
β-strand	709	1	98
α-helix	710-724	15
α-helix	744-752	9

Chain 1: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	171-176	6
α-helix	178-187	10
α-helix	189-195	7
α-helix	196-200	5
α-helix	206-212	7
α-helix	214-225	12
α-helix	252-262	11
α-helix	264-272	9
α-helix	280-294	15
α-helix	315-318	4
α-helix	372-388	17
α-helix	468-482	15
α-helix	497-515	19
α-helix	541-566	26
α-helix	576-604	29
α-helix	607-638	32

Chain 2: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	19-26	8
α-helix	29-38	10
α-helix	41-52	12
α-helix	59-65	7
α-helix	71-83	13
β-strand	87-88	2	119
β-strand	99-100	2	119
α-helix	102-112	11
β-strand	124	1	120
α-helix	136-146	11
α-helix	147-152	6
α-helix	161-169	9
α-helix	186-193	8
α-helix	197-210	14
α-helix	218-230	13
β-strand	234	1	120
α-helix	244-256	13
β-strand	261	1	120
α-helix	263-265	3
β-strand	269	1	120
α-helix	273-279	7
α-helix	354-361	8
β-strand	369	1	121
β-strand	374	1	121
α-helix	380-388	9
α-helix	395-402	8
α-helix	405-407	3
α-helix	409-413	5
α-helix	435-449	15
β-strand	452-454	3	118
β-strand	457-458	2	117
α-helix	465-478	14
β-strand	492-493	2	117
α-helix	495-506	12

Chain 3: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	76-90	15
α-helix	92-94	3
α-helix	103-122	20
α-helix	129-144	16

Chain 4: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	101
α-helix	34-37	4
α-helix	39-42	4
α-helix	51-67	17
β-strand	73-78	6	101
β-strand	83-85	3	101
α-helix	117-134	18
α-helix	138-142	5
α-helix	149-166	18
β-strand	175-182	8	101
α-helix	193-205	13
α-helix	209	1
β-strand	210-216	7	101
α-helix	222-231	10
β-strand	234-236	3	101
α-helix	244-251	8
α-helix	274-276	3
β-strand	287-288	2	102
β-strand	295-296	2	102
β-strand	312	1	103
α-helix	314-322	9

Chain 5: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	117
β-strand	8-11	4	118
α-helix	14-25	12
β-strand	31-34	4	118
β-strand	39-42	4	118
α-helix	47-62	16

Chain 6: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	124-129	6	104
α-helix	134-137	4
α-helix	145-163	19
β-strand	168-175	8	104
β-strand	178-186	9	104
α-helix	189-201	13
α-helix	210-220	11
β-strand	229-234	6	104
α-helix	247-256	10
β-strand	260-263	4	104
β-strand	265	1	105
α-helix	271-280	10
β-strand	290	1	105
α-helix	294-305	12
β-strand	317	1	103
β-strand	322-323	2	106
β-strand	326-327	2	107
β-strand	346-348	3	107
β-strand	355-357	3	107
α-helix	361-363	3
β-strand	369-370	2	106
α-helix	374-383	10
α-helix	385-388	4
β-strand	390-391	2	108
β-strand	427-428	2	108
α-helix	438-444	7
α-helix	452-455	4

Chain 7: 34 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	105-108	4
α-helix	122-124	3
α-helix	125-127	3
β-strand	132	1	109
β-strand	133	1	110
β-strand	142	1	110
α-helix	150-160	11
β-strand	162-165	4	111
β-strand	172-174	3	111
α-helix	179-186	8
α-helix	190-200	11
β-strand	201	1	109
α-helix	207-214	8
α-helix	215-219	5
β-strand	226	1	112
β-strand	233	1	112
α-helix	239-247	9
β-strand	255	1	113
α-helix	263	1
α-helix	264-268	5
β-strand	317	1	112
β-strand	318	1	113
α-helix	323-332	10
β-strand	341	1	114
α-helix	350-352	3
α-helix	364-374	11
β-strand	379	1	114
β-strand	382-383	2	115
α-helix	392-403	12
β-strand	407-411	5	115
α-helix	414-423	10
β-strand	437	1	115
β-strand	453-456	4	115
α-helix	457-460	4
α-helix	468-479	12
β-strand	484-488	5	115
α-helix	490-492	3
α-helix	496-505	10
β-strand	511-513	3	115
α-helix	527-531	5
α-helix	540-543	4
β-strand	552-559	8	116
α-helix	563-571	9
α-helix	575-579	5
α-helix	585-600	16
β-strand	605-608	4	116
α-helix	613-620	8
α-helix	633-640	8
α-helix	641-645	5
β-strand	651-654	4	116
α-helix	656-658	3
α-helix	664-666	3
β-strand	669-672	4	116
α-helix	680-690	11
β-strand	703-710	8	116
α-helix	715-728	14
β-strand	733	1	116
α-helix	742-744	3
α-helix	753-763	11

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
Transcription initiation factor IIF subunit alpha	Q	protein	735	Saccharomyces cerevisiae	P41895 (AlphaFold model)
Transcription initiation factor IIF subunit beta	R	protein	398	Saccharomyces cerevisiae	P41896 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae	P20433 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB7	G	protein	171	Saccharomyces cerevisiae	P34087 (AlphaFold model)
Transcription initiation factor IIB	M	protein	345	Saccharomyces cerevisiae	P29055
DNA-directed RNA polymerase subunit	A	protein	1733	Saccharomyces cerevisiae	P04050
DNA-directed RNA polymerase subunit beta	B	protein	1224	Saccharomyces cerevisiae	P08518
DNA-directed RNA polymerase II subunit RPB3	C	protein	318	Saccharomyces cerevisiae	P16370
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 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

19 more molecules are not listed.

Sequence of entity 1 (Q), FASTA

>7ML4_1 Transcription initiation factor IIF subunit alpha (chains Q)
MSRRNPPGSRNGGGPTNASPFIKRDRMRRNFLRMRMGQNGSNSSSPGVPNGDNSRGSLVK
KDDPEYAEEREKMLLQIGVEADAGRSNVKVKDEDPNEYNEFPLRAIPKEDLENMRTHLLK
FQSKKKINPVTDFHLPVRLHRKDTRNLQFQLTRAEIVQRQKEISEYKKKAEQERSTPNSG
GMNKSGTVSLNNTVKDGSQTPTVDSVTKDNTANGVNSSIPTVTGSSVPPASPTTVSAVES
NGLSNGSTSAANGLDGNASTANLANGRPLVTKLEDAGPAEDPTKVGMVKYDGKEVTNEPE
FEEGTMDPLADVAPDGGGRAKRGNLRRKTRQLKVLDENAKKLRFEEFYPWVMEDFDGYNT
WVGSYEAGNSDSYVLLSVEDDGSFTMIPADKVYKFTARNKYATLTIDEAEKRMDKKSGEV
PRWLMKHLDNIGTTTTRYDRTRRKLKAVADQQAMDEDDRDDNSEVELDYDEEFADDEEAP
IIDGNEQENKESEQRIKKEMLQANAMGLRDEEAPSENEEDELFGEKKIDEDGERIKKALQ
KTELAALYSSDENEINPYLSESDIENKENESPVKKEEDSDTLSKSKRSSPKKQQKKATNA
HVHKEPTLRVKSIKNCVIILKGDKKILKSFPEGEWNPQTTKAVDSSNNASNTVPSPIKQE
EGLNSTVAEREETPAPTITEKDIIEAIGDGKVNIKEFGKFIRRKYPGAENKKLMFAIVKK
LCRKVGNDHMELKKE

Sequence of entity 2 (R), FASTA

>7ML4_2 Transcription initiation factor IIF subunit beta (chains R)
MSSGSAGAPALSNNSTNSVAKEKSGNISGDEYLSQEEEVFDGNDIENNETKVYEESLDLD
LERSNRQVWLVRLPMFLAEKWRDRNNLHGQELGKIRINKSKITLLLNENDNDSIPHEYDL
ELTKKVVENEYVFTEQNLKKYQQRKKELEADPEKQRQAYLKKQEREEELKKKQQQQKRRN
NRKKFNHRVMTDRDGRDRYIPYVKTIPKKTAIVGTVCHECQVMPSMNDPNYHKIVEQRRN
IVKLNNKERITTLDETVGVTMSHTGMSMRSDNSNFLKVGREKAKSNIKSIRMPKKEILDY
LFKLFDEYDYWSLKGLKERTRQPEAHLKECLDKVATLVKKGPYAFKYTLRPEYKKLKEEE
RKATLGELADEQTGSAGDNAQGDAEADLEDEIEMEDVV

Sequence of entity 3 (D), FASTA

>7ML4_3 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 4 (G), FASTA

>7ML4_4 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 5 (M), FASTA

>7ML4_5 Transcription initiation factor IIB (chains M)
MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTR
SEWRTFSNDDHNGDDPSRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMD
KKDNEVQAAFAKITMLCDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGC
RRAEVARTFKEIQSLIHVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIP
RFCSHLGLPMQVTTSAEYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQ
TLQVTEGTIKSGYKILYEHRDKLVDPQLIANGVVSLDNLPGVEKK

Sequence of entity 6 (A), FASTA

>7ML4_6 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 7 (B), FASTA

>7ML4_7 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 8 (C), FASTA

>7ML4_8 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 9 (E), FASTA

>7ML4_9 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 10 (F), FASTA

>7ML4_10 DNA-directed RNA polymerases I,II,and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 11 (H), FASTA

>7ML4_11 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 12 (I), FASTA

>7ML4_12 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	15

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 P41895 (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
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
7UI9 3.3 Å, Core Mediator-PICearly (Copy A)
7UIO 3.3 Å, Mediator-PIC Early (Composite Model)
7ML2 3.4 Å, RNA polymerase II pre-initiation complex (PIC3)
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…
5IP7 3.52 Å, Structure of RNA Polymerase II-Tfg1 peptide complex

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