5OQM: DNA-directed RNA polymerase II subunit RPB1

Name: PDB 5OQM: Structure of yeast transcription pre-initiation complex with tfiih and core mediator
Published: 2018-05-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Structure of yeast transcription pre-initiation complex with tfiih and core mediator. Determined by electron microscopy at 5.8 Å resolution. Released 9 May 2018.

Method: Electron microscopy
Resolution: 5.8 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct, Saccharomyces cerevisiae
Chains: 46
Atoms: 79,757
Mol. weight: 1811.06 kDa
Ligands: ZN, MG, SF4
Released: 9 May 2018

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

Secondary structure: helices and β-sheets

5OQM contains 470 α-helices and 441 β-strands across 44 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: 32 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	19-33	15
β-strand	37-41	5	113
α-helix	42-43	2
α-helix	48-62	15
β-strand	69-73	5	113
α-helix	76-95	20
β-strand	106	1	113
α-helix	117-119	3
α-helix	129-144	16
α-helix	165-173	9
α-helix	179-188	10
α-helix	192-200	9
β-strand	206-209	4	113
α-helix	210-213	4
α-helix	219-225	7
β-strand	231-235	5	113
α-helix	240-246	7
β-strand	251-253	3	114
α-helix	255-276	22
α-helix	280-300	21
α-helix	312-315	4
α-helix	328-346	19
β-strand	352-353	2	114
α-helix	356-366	11
α-helix	373-387	15
α-helix	393-410	18
β-strand	417-420	4	114
β-strand	434-438	5	114
α-helix	442-446	5
α-helix	449-452	4
β-strand	456-460	5	113
α-helix	468-471	4
β-strand	478-480	3	113
α-helix	488-490	3
β-strand	491-492	2	115
β-strand	494-496	3	116
α-helix	504-507	4
α-helix	516-532	17
β-strand	537-541	5	115
α-helix	544-550	7
α-helix	558-562	5
β-strand	568-569	2	115
α-helix	576-590	15
β-strand	597-601	5	115
β-strand	619-622	4	115
α-helix	633-646	14
α-helix	656-669	14
β-strand	677-681	5	115
α-helix	684-688	5
β-strand	697-699	3	116
α-helix	701-722	22

Chain 1: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	111
β-strand	12-19	8	111
β-strand	26-31	6	111
β-strand	37-41	5	111
α-helix	42-44	3
β-strand	45-50	6	111
β-strand	59-64	6	111
α-helix	82-84	3
β-strand	85-90	6	111
α-helix	94-120	27
α-helix	171-176	6
α-helix	178-187	10
α-helix	189-199	11
α-helix	206-224	19
α-helix	230-239	10
β-strand	246-250	5	110
α-helix	252-262	11
α-helix	264-273	10
α-helix	280-286	7
α-helix	287-291	5
α-helix	292-295	4
α-helix	309-329	21
α-helix	371-393	23
α-helix	467-482	16
α-helix	487-489	3
α-helix	496-516	21
α-helix	543-570	28
α-helix	576-604	29
α-helix	607-638	32

Chain 2: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
α-helix	19-25	7
α-helix	28-37	10
α-helix	41-50	10
β-strand	57-58	2	117
α-helix	59-66	8
α-helix	71-83	13
β-strand	87-91	5	117
β-strand	96-100	5	117
α-helix	102-112	11
α-helix	117-122	6
α-helix	132-151	20
α-helix	161-169	9
β-strand	173-176	4	118
β-strand	181-184	4	118
α-helix	186-194	9
α-helix	197-210	14
α-helix	216-224	9
α-helix	237-240	4
α-helix	244-256	13
β-strand	259-262	4	119
β-strand	266-271	6	119
α-helix	273-280	8
α-helix	381-388	8
α-helix	394-403	10
α-helix	408-418	11
α-helix	435-449	15
β-strand	452-460	9	58
α-helix	465-477	13
β-strand	481-485	5	58
β-strand	490-494	5	58
α-helix	498-507	10

Chain 3: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	28-30	3	120
β-strand	37-39	3	120
α-helix	40-49	10
β-strand	53	1	121
β-strand	62	1	121
α-helix	63-64	2
α-helix	76-92	17
α-helix	104-122	19
α-helix	128-144	17

Chain 4: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	24-31	8	31
α-helix	34-40	7
α-helix	50-67	18
β-strand	72-79	8	31
β-strand	82-85	4	31
α-helix	90-96	7
α-helix	108-111	4
α-helix	116-135	20
α-helix	138-142	5
α-helix	149-166	18
β-strand	173-182	10	31
α-helix	190-206	17
β-strand	210-216	7	31
α-helix	222-230	9
β-strand	235-240	6	31
α-helix	244-254	11
β-strand	285-288	4	32
β-strand	296	1	32
α-helix	305-307	3
α-helix	311-313	3
α-helix	314-320	7

Chain 5: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	58
α-helix	14-27	14
β-strand	31-34	4	58
β-strand	39-42	4	58
α-helix	44-46	3
α-helix	47-62	16

Chain 6: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	124-131	8	64
α-helix	134-137	4
α-helix	145-163	19
β-strand	168-175	8	64
β-strand	178-186	9	64
α-helix	189-199	11
α-helix	210-221	12
β-strand	229-236	8	64
α-helix	247-256	10
β-strand	260-266	7	64
α-helix	271-279	9
β-strand	288-291	4	64
α-helix	294-305	12
β-strand	319-323	5	32
β-strand	326-328	3	65
β-strand	346-348	3	65
β-strand	355-356	2	65
β-strand	362	1	32
β-strand	369-370	2	32
α-helix	373-383	11
α-helix	388-389	2
β-strand	390-392	3	66
α-helix	394-397	4
α-helix	418-421	4
β-strand	426-429	4	66
β-strand	434-436	3	66
α-helix	438-446	9
α-helix	452-455	4

Chain 7: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	364-375	12
β-strand	380-385	6	68
α-helix	392-403	12
β-strand	406-411	6	68
α-helix	414-427	14
β-strand	435	1	68
β-strand	438	1	69
β-strand	443	1	69
β-strand	451-456	6	68
α-helix	457-461	5
α-helix	470-478	9
β-strand	484-488	5	68
α-helix	490-492	3
α-helix	496-503	8
β-strand	509-514	6	68
α-helix	524-526	3
α-helix	527-530	4
β-strand	534-537	4	68
α-helix	540-546	7
β-strand	551-559	9	70
α-helix	563-571	9
α-helix	574-577	4
α-helix	578-581	4
α-helix	585-601	17
β-strand	605-608	4	70
α-helix	612-622	11
β-strand	626-627	2	70
α-helix	633-645	13
β-strand	651-654	4	70
α-helix	656-660	5
β-strand	669-672	4	70
α-helix	680-693	14
β-strand	702-710	9	70
α-helix	716-728	13
β-strand	732-736	5	70
α-helix	742-744	3
α-helix	753-769	17

36 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 polymerase II subunit RPB4	D	protein	221	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20433 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	protein	215	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20434
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	155	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20435
DNA-directed RNA polymerase II subunit RPB7	G	protein	171	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P34087
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

34 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>5OQM_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

>5OQM_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

>5OQM_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW

Sequence of entity 4 (D), FASTA

>5OQM_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIK
EALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETRE
KELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQL
GSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Sequence of entity 5 (E), FASTA

>5OQM_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Sequence of entity 6 (F), FASTA

>5OQM_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Sequence of entity 7 (G), FASTA

>5OQM_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Sequence of entity 8 (H), FASTA

>5OQM_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR

Sequence of entity 9 (I), FASTA

>5OQM_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS

Sequence of entity 10 (J), FASTA

>5OQM_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD

Sequence of entity 11 (K), FASTA

>5OQM_11 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Sequence of entity 12 (L), FASTA

>5OQM_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	16
MG	Magnesium ion	Mg	1
SF4	Iron/sulfur cluster	Fe4 S4	1

Primary citation

Structures of transcription pre-initiation complex with TFIIH and Mediator. Schilbach, S., Hantsche, M., Tegunov, D. et al. Nature (2017) 551:204-209. DOI 10.1038/nature24282 · 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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