7UIL: Mediator-PIC Early

Name: PDB 7UIL: Mediator-PIC Early (Tail A/B Dimer)
Published: 2023-02-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Mediator-PIC Early (Tail A/B Dimer). Determined by electron microscopy at 4.3 Å resolution. Released 15 Feb 2023.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Saccharomyces cerevisiae
Chains: 13
Atoms: 37,614
Mol. weight: 1214.61 kDa
Released: 15 Feb 2023

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

Secondary structure: helices and β-sheets

7UIL contains 220 α-helices and 152 β-strands across 13 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.

Chains 1 and b: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-50	22
α-helix	67-103	37

Chains 2 and c: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	11-18	8
α-helix	21-23	3
α-helix	24-55	32
α-helix	64-94	31
α-helix	96-99	4
α-helix	101-109	9

Chains 3 and e: 43 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	288-304	17
α-helix	313-324	12
α-helix	335-355	21
α-helix	368-375	8
α-helix	376-380	5
α-helix	381-386	6
α-helix	393-401	9
α-helix	405-418	14
α-helix	439-449	11
α-helix	458-461	4
β-strand	479-482	4	22
β-strand	488-491	4	22
α-helix	494-504	11
α-helix	507-509	3
α-helix	521-527	7
α-helix	529-531	3
α-helix	534-554	21
α-helix	557-569	13
α-helix	574-579	6
α-helix	584-597	14
α-helix	600-603	4
α-helix	612-636	25
α-helix	641-647	7
α-helix	657-663	7
α-helix	683-697	15
α-helix	698-702	5
α-helix	707-712	6
α-helix	715-735	21
α-helix	742-749	8
α-helix	750-752	3
α-helix	757-760	4
α-helix	761-776	16
α-helix	781-795	15
α-helix	805-814	10
α-helix	816-824	9
α-helix	847-858	12
α-helix	868-871	4
α-helix	895-908	14
α-helix	917-927	11
α-helix	929-946	18
α-helix	959-974	16
α-helix	981-991	11
α-helix	1079-1082	4
α-helix	1088-1105	18
α-helix	1110-1129	20

Chains 4 and n: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	835-849	15
β-strand	856-860	5	23
β-strand	864-868	5	23
β-strand	880-886	7	23
β-strand	891-898	8	23
α-helix	903-907	5
α-helix	908-913	6
α-helix	918-942	25
β-strand	956-963	8	24
β-strand	966-973	8	24
β-strand	978-991	14	24
β-strand	994-1002	9	24
α-helix	1016-1025	10
β-strand	1050	1	24
β-strand	1054-1057	4	24
α-helix	1059-1073	15

Chains 5 and o: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	849-875	27
α-helix	880-892	13
α-helix	907-914	8
α-helix	920-922	3
α-helix	923-931	9
β-strand	938-939	2	25
β-strand	942-943	2	25

Chains 6 and p: 42 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	26
β-strand	16-19	4	26
β-strand	28-31	4	26
β-strand	33-35	3	27
β-strand	41-43	3	27
α-helix	44-46	3
β-strand	47-49	3	26
β-strand	101-102	2	28
β-strand	105-110	6	29
β-strand	120-125	6	29
β-strand	130-135	6	29
β-strand	148-154	7	29
β-strand	159-161	3	29
α-helix	173-174	2
β-strand	178-179	2	28
β-strand	190-195	6	30
β-strand	197	1	31
β-strand	202-211	10	32
β-strand	216-224	9	32
β-strand	230	1	31
β-strand	235-243	9	30
β-strand	247-254	8	30
β-strand	260-266	7	30
α-helix	273-276	4
β-strand	281-288	8	33
β-strand	294-301	8	33
β-strand	306-315	10	33
α-helix	327-329	3
β-strand	330-339	10	33
α-helix	340-342	3
β-strand	344	1	34
β-strand	350	1	34
β-strand	353-358	6	35
β-strand	371-377	7	35
β-strand	384-392	9	35
β-strand	426-435	10	35
β-strand	439-444	6	36
α-helix	445	1
β-strand	450-455	6	36
β-strand	460-464	5	36
β-strand	470	1	36
α-helix	474-477	4
β-strand	485-488	4	32
α-helix	491-493	3
β-strand	497-498	2	37
α-helix	501-503	3
α-helix	504-506	3
β-strand	507-512	6	38
β-strand	518-523	6	38
β-strand	532-533	2	38
β-strand	534-535	2	37
α-helix	542-544	3
α-helix	545-561	17
α-helix	567-583	17
α-helix	585-602	18
α-helix	611-618	8
α-helix	623-633	11
α-helix	641-675	35
α-helix	683-722	40
α-helix	727-729	3
α-helix	731-737	7
α-helix	739-761	23
α-helix	768-770	3
α-helix	771-782	12
α-helix	788-808	21
α-helix	813-816	4
α-helix	817-821	5
α-helix	826-828	3
α-helix	829-842	14
α-helix	844-846	3
α-helix	849-854	6
α-helix	864-866	3
β-strand	868	1	39
α-helix	879-881	3
β-strand	884	1	27
α-helix	887-889	3
α-helix	892-894	3
α-helix	897-899	3
β-strand	901	1	39
β-strand	905	1	40
β-strand	912	1	40
α-helix	913-914	2
α-helix	915-919	5
β-strand	924-926	3	41
β-strand	932-933	2	41
α-helix	938-940	3
α-helix	941-943	3
α-helix	955-959	5
β-strand	962	1	42
α-helix	967	1
β-strand	968	1	42
β-strand	969-971	3	41
α-helix	972-973	2

Chain a: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	7-21	15
α-helix	28-37	10
β-strand	41-46	6	43
β-strand	51-57	7	43
β-strand	61-68	8	43
β-strand	73-81	9	43
β-strand	91	1	44
β-strand	102	1	44
α-helix	103-109	7
α-helix	115-130	16
α-helix	164-181	18
β-strand	187-190	4	45
β-strand	198-203	6	45
β-strand	209-219	11	45
β-strand	227-229	3	46
β-strand	232-234	3	47
β-strand	239-241	3	47
β-strand	248-250	3	46
β-strand	252-258	7	45
β-strand	272-274	3	48
α-helix	280-282	3
β-strand	283-286	4	45
α-helix	298-304	7
β-strand	312-316	5	49
β-strand	322-324	3	48
β-strand	325-329	5	45
α-helix	332-336	5
α-helix	337-347	11
α-helix	348-352	5
α-helix	353-360	8
β-strand	528-532	5	49
β-strand	536-539	4	49
β-strand	543-546	4	49
α-helix	551-565	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mediator of RNA polymerase II transcription subunit 2	1, b	protein	431	Saccharomyces cerevisiae	Q12124 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 3	2, c	protein	397	Saccharomyces cerevisiae	P40356 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 5	3, e	protein	1132	Saccharomyces cerevisiae	P53114 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 14	4, n	protein	1082	Saccharomyces cerevisiae	P19263 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 15	5, o	protein	1081	Saccharomyces cerevisiae	P19659
Mediator of RNA polymerase II transcription subunit 16	6, p	protein	974	Saccharomyces cerevisiae	P32259
Mediator of RNA polymerase II transcription subunit 1	a	protein	566	Saccharomyces cerevisiae	Q12321

Sequence of entity 1 (1, b), FASTA

>7UIL_1 Mediator of RNA polymerase II transcription subunit 2 (chains 1, b)
MVVQNSPVSSVHTANFSERGSNTRTMTYKNKLTVCFDDILKVGAEMMMQQQLKNVQLDSY
LVNGFSQSQQKLLKEKVKLFHGILDDLETSLSQSSSYLETLTALGKEKEKEREEAEKKRA
EQENMRKVREQEELKKRQELEEASQQQQLQQNSKEKNGLGLNFSTTAPANTTDANGSKEN
YQELGSLQSSSQTQLENANAANNGAAFSPLTTTRIQSQQAQPSDVMFNDLNSMDISMFSG
LDSTGFDSTAFNATVDETKGFDDNDSGNNYNDINISSIENNINNNINSTKNGKDNNNESN
KNNNGDEKNKNNNEDNENNNNSSEKNNNNNNNNNNNNDDNGNNNNNNSGNDNNNTTNNDS
NNKNNSITTGNDNENIVNNDLPTTVVSNPGDNPPPADNGEEYLTLNDFNDLNIDWSTTGD
NGELDLSGFNI

Sequence of entity 2 (2, c), FASTA

>7UIL_2 Mediator of RNA polymerase II transcription subunit 3 (chains 2, c)
MDSIIPAGVKLDDLQVILAKNENETRDKVCKQINEARDEILPLRLQFNEFIQIMANIDQE
GSKQADRMAKYLHIRDKILQLNDRFQTLSSHLEALQPLFSTVPEYLKTADNRDRSFQLLE
PLSTYNKNGNAVCSTATVVSTNHSAAASTPTTTATPHANPITHAHSLSNPNSTATMQHNP
LAGKRGPKSGSTMGTPTVHNSTAAAPIAAPKKPRKPRQTKKAKAQAQAQAQAQAQVYAQQ
STVQTPITASMAAALPNPTPSMINSVSPTNVMGTPLTNMMSPMGNAYSMGAQNQGGQVSM
SQFNGSGNGSNPNTNTNSNNTPLQSQLNLNNLTPANILNMSMNNDFQQQQQQQQQQQQPQ
PQYNMNMGMNNMNNGGKELDSLDLNNLELGGLNMDFL

Sequence of entity 3 (3, e), FASTA

>7UIL_3 Mediator of RNA polymerase II transcription subunit 5 (chains 3, e)
MEKESVYNLALKCAERQLTSMEFSNLYKEFFNEKFPSLIQEEEEDTTTTANINEVKKASD
LVDTPSNNTAATADTTHLHEALDIVCSDFVKILNLEKPLILADYIVEVLLVNYNSDMIKC
FLPKLNSVRNSLLLAHFFSKSCSFFAKLSDTLIIDQVRKDLGNVIVPNILSLDMNSMNKE
LIAIVSKLLQTTLKLSPSPILLTSAGCKNGSFTLLNQLSQTNKLLFKRVSQTFEAKLHFK
DTKPFLNKDSTNEFVGSPSLTSPQYIPSPLSSTKPPGSVNSAAKYKDMKLLRYYKNIWLN
NKIINWEISNPDFLSKYSAITSSIFQESFNSVQNLDQLLTDLIETSFTCFAQFVSNKQYH
QANSNLTLLERKWVIFITKHLPLLILENSSRSPRVVTNALDNIDEKVVKAIRIYFTEKDD
NKTNNEDLFDDYPSTSLDIRHDFIKGLIMLNLQPASVINNYLREDQMIDTSILPTRDDLF
VRNLQGIQEVVHNTNSFIISSLDTLELESITESITHDSSNGLFQVLHNFESVAPTKQREI
VKAFLSIFEDAIKELNYNRIAKICALLFFNFSHSLTTILSFSSPAALMKTLIKFVDLSRN
GRNGSNGNDESSEYETINISLSFSWAILLIINLTQTYGISVVDVALKYPELSIKNSFIIN
FISNLPNVSDKYYLEESNVNDSDMLTKSHNTVQSWLCDLFVNGSITDQLIQNIETRQLAN
LIPFIVKQVLLSVEIGVLTDISSLIGGFEYFLQPLLLVGLIKTFYWLEQFLSCVKNDTIS
EDILQGIFNLLNTLFNPVTLNEDSKAFHTAVLRLNAIPLLKVLRKFRVQSQSNYGIYSSD
AQGDPNLEPLIAKLVAVLNVSPVYDVDPRIINSENDYSRKQLGYGKFLILNENPINKIMT
NQINSFWSLHSSTYYNLDYLFELIELVTPKSFLFDVLKTLEYKLATYGVPGSENKRGSLD
SEHVFDYFFYFLVLYDVKTAEEASQLIEYMENDAKKSKGDVDIKGEDLHEKNDSAEVRQE
TQPKAEATQDDDFDMLFGENDTSTQAYEEEEENEDNDGNNRTNNVPMIKAEETPSKTNKI
SILKRHSFAVLLHERKLLNDLALENGEITKTENEKFISYHDKYLCMLKTCVF

Sequence of entity 4 (4, n), FASTA

>7UIL_4 Mediator of RNA polymerase II transcription subunit 14 (chains 4, n)
MTTTIGSPQMLANEERLSNEMHALKNRSEQNGQEQQGPVKNTQLHGPSATDPETTATQKE
SLEMVPKDTSAATMTSAPPPALPHVEINQVSLALVIRNLTVFTMKELAQYMKTNVHTQAN
EPNSAKKIRFLQLIIFLRTQFLKLYVLVKWTRTIKQNNFHVLIDLLNWFRTTNMNVNNCI
WALKSSLNSMTNAKLPNVDLVTALEVLSLGRPNLPTHNFKLSGVSNSMDMVDGMAKVPIG
LILQRLKDLNLTVSIKIALMNIPKPLNSYHIKNGRIYFTVPNEFEIQLSTVNRQSPLFFV
DLKLLFNTEAEQTVSAVTEATSTNGDSENNEENSSSNGNNLPLNKPRLEKLINEILLKSN
DPLLSLYNFLHKYVLTLQLYMVHREFLKLANGGKFSKSNLIHNYDSKKSTITVRYWLNGK
MDSKGKITIGIQRTTESLILKWDNQSASRAKNMPVIYNNIVSNIEGILDEIMFNHARIIR
SELLARDIFQEDEENSDVLLFQLPTTCVSMAPIQLKIDLLSGQFYFRNPTPLLSNYASKI
NRAEGPEELARILQQLKLDKIIHVLTTMFENTGWSCSRIIKIDKPIRTQVNTGGESVVKK
EDNKYAIAGNSTTNSDVSLLLQRDLFIRLPHWPLNWYLILSIISSKTSCVVEKRIGKIVS
QRGKWNLKYLDNSNVMTVKLESITYQKIMILQRTILNRIINHMLIDSLNQLEIRNKICSS
EMINEQKLPQYIIQGSNTNDNISIITLELESFLEGSKALNSILESSMFLRIDYSNSQIRL
YAKFKRNTMMIQCQIDKLYIHFVQEEPLAFYLEESFTNLGIIVQYLTKFRQKLMQLVVLT
DVVERLHKNFESENFKIIALQPNEISFKYLSNNDEDDKDCTIKISTNDDSIKNLTVQLSP
SNPQHIIQPFLDNSKMDYHFIFSYLQFTSSLFKALKVILNERGGKFHESGSQYSTMVNIG
LHNLNEYQIVYYNPQAGTKITICIELKTVLHNGRDKIQFHIHFADVAHITTKSPAYPMMH
QVRNQVFMLDTKRLGTPESVKPANASHAIRLGNGVACDPSEIEPILMEIHNILKVDSNSS
SS

Sequence of entity 5 (5, o), FASTA

>7UIL_5 Mediator of RNA polymerase II transcription subunit 15 (chains 5, o)
MSAAPVQDKDTLSNAERAKNVNGLLQVLMDINTLNGGSSDTADKIRIHAKNFEAALFAKS
SSKKEYMDSMNEKVAVMRNTYNTRKNAVTAAAANNNIKPVEQHHINNLKNSGNSANNMNV
NMNLNPQMFLNQQAQARQQVAQQLRNQQQQQQQQQQQQRRQLTPQQQQLVNQMKVAPIPK
QLLQRIPNIPPNINTWQQVTALAQQKLLTPQDMEAAKEVYKIHQQLLFKARLQQQQAQAQ
AQANNNNNGLPQNGNINNNINIPQQQQMQPPNSSANNNPLQQQSSQNTVPNVLNQINQIF
SPEEQRSLLQEAIETCKNFEKTQLGSTMTEPVKQSFIRKYINQKALRKIQALRDVKNNNN
ANNNGSNLQRAQNVPMNIIQQQQQQNTNNNDTIATSATPNAAAFSQQQNASSKLYQMQQQ
QQAQAQAQAQAQAQAQAQAQAQAAQAAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQ
AHAQHQPSQQPQQAQQQPNPLHGLTPTAKDVEVIKQLSLDASKTNLRLTDVTNSLSNEEK
EKIKMKLKQGQKLFVQVSNFAPQVYIITKNENFLKEVFQLRIFVKEILEKCAEGIFVVKL
DTVDRLIIKYQKYWESMRIQILRRQAILRQQQQMANNNGNPGTTSTGNNNNIATQQNMQQ
SLQQMQHLQQLKMQQQQQQQQQQQQQQQQQQQQQQQHIYPSSTPGVANYSAMANAPGNNI
PYMNHKNTSSMDFLNSMENTPKVPVSAAATPSLNKTINGKVNGRTKSNTIPVTSIPSTNK
KLSISNAASQQPTPRSASNTAKSTPNTNPSPLKTQTKNGTPNPNNMKTVQSPMGAQPSYN
SAIIENAFRKEELLLKDLEIRKLEISSRFKHRQEIFKDSPMDLFMSTLGDCLGIKDEEML
TSCTIPKAVVDHINGSGKRKPTKAAQRARDQDSIDISIKDNKLVMKSKFNKSNRSYSIAL
SNVAAIFKGIGGNFKDLSTLVHSSSPSTSSNMDVGNPRKRKASVLEISPQDSIASVLSPD
SNIMSDSKKIKVDSPDDPFMTKSGATTSEKQEVTNEAPFLTSGTSSEQFNVWDWNNWTSA
T

Sequence of entity 6 (6, p), FASTA

>7UIL_6 Mediator of RNA polymerase II transcription subunit 16 (chains 6, p)
MMLGEHLMSWSKTGIIAYSDSQSSNANICLTFLESINGINWRFHTPQKYVLHPQLHEVQY
QESSSTLSTHSTTTSVNGSTTAGVGSTPNFGGNSNKSPPQFFYNISSIHWNNWFSLPGDM
LAVCDELGNMTMLITGQRPDRATTYEKLTMVFQDNVYKIYNHVMPLKPVDKLKPMNIERK
QTRKEYNTSILEFRWLTSSKSVIVSQFCAFDSSSNTYRSRAQQVPPYGVYHPPFIKYACL
AIRKNGQIDFWYQFSNSKDHKKITLQLLDTSNQRFKDLQWLEFARITPMNDDQCMLITTY
SKLSKNISFYKLHVNWNLNATKPNVLNDPSLKIQFILSTTLDPTDDEGHVLKLENLHVVS
KSSIEKDPSPEILVLYNVCDTSKSLVKRYRLAPTQLSAEYLVILKPDLNIDRNNSTNQIF
QSRRYNLRRHSDIVLDKKVTLITSEMFDAFVSFYFEDGTIESYNQNDWKLETERLISQSQ
LGKFKNIIASPLSAGFNYGKLPLPPSVEWMKVSPSMCGVIVKQYNKKWPQFYAAVQKNYA
DPEKDSINATALAFGYVKSLHKQISAEDLTIAAKTHILRISFLDRKRAKEFITTLLKSLY
SFFNISPDAPKEIMDKIITSRPLQKIMLLQLELGSCFSQENIEEMARVILYLKNVLFAFN
GVARNFHFAIEQISNNSNQQQNPKLFQTIFSKQDLIHSLIPVAKWFVKFITYLTQEILIL
INDPTNKEYTLVHGIFGAKMSRTLILSILNEIKKVTQIVAKFPETSYPILNESSTFLKLV
LSESPVDFEKFETFLVDVNNKFIALCEQQPSQEREFSLLVKAEIPPEYAKVGDFLLQYAN
NAVISHANAAAVYFADTSGLKISNSEFFNPEIFHLLQPLEEGLIIDTDKLPIKNRTSKSF
SKLLYDDVTCDKLSVSEISDGKLKRCSRCGSVTRAGNIISSDKTIVPTSIQTKRWPTMYT
RLCICSGMLFEMDG

Sequence of entity 7 (a), FASTA

>7UIL_7 Mediator of RNA polymerase II transcription subunit 1 (chains a)
MVEGDSYVETLDSMIELFKDYKPGSITLENITRLCQTLGLESFTEELSNELSRLSTASKI
IVIDVDYNKKQDRIQDVKLVLASNFDNFDYFNQRDGEHEKSNILLNSLTKYPDLKAFHNN
LKFLYLLDAYSHIESDSTSHNNGSSDKSLDSSNASFNNQGKLDLFKYFTELSHYIRQCFQ
DNCCDFKVRTNLNDKFGIYILTQGINGKEVPLAKIYLEENKSDSQYRFYEYIYSQETKSW
INESAENFSNGISLVMEIVANAKESNYTDLIWFPEDFISPELIIDKVTCSSNSSSSPPII
DLFSNNNYNSRIQLMNDFTTKLINIKKFDISNDNLDLISEILKWVQWSRIVLQNVFKLVS
TPSSNSNSSELEPDYQAPFSTSTKDKNSSTSNTEPIPRSNRHGSVVEASRRRRSSTNKSK
RPSITEAMMLKEEGLQQFNLHEILSEPAIEEENGDSIKEHSTTMDGANDLGFTASVSNQE
NAGTDIVMEDHGVLQGTSQNYGTATADDADIEMKDVSSKPSKPESSVLQLIVSEDHIILD
TISECNLYDDVKCWSKFIEKFQDIVS

Primary citation

Structural basis of a transcription pre-initiation complex on a divergent promoter. Gorbea Colon, J.J., Palao 3rd, L., Chen, S.F. et al. Mol Cell (2023) 83:574. DOI 10.1016/j.molcel.2023.01.011 · PubMed

Other PDB entries of the same protein (UniProt Q12124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UIO 3.3 Å, Mediator-PIC Early (Composite Model)
7UIC 3.7 Å, Mediator-PIC Early (Tail A)
7UIK 7.7 Å, Mediator-PIC Early (Tail A + Upstream DNA & Activator)
8ZZ3 Molecular architecture of the yeast Mediator complex

Browse structure collections

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