7UIK: Mediator-PIC Early

Mediator-PIC Early (Tail A + Upstream DNA & Activator). Determined by electron microscopy at 7.7 Å resolution. Released 1 Mar 2023.

Method
Electron microscopy
Resolution
7.7 Å
Organisms
Saccharomyces cerevisiae, Saccharomyces cerevisiae S288C
Chains
10
Atoms
20,237
Mol. weight
536.32 kDa
Ligands
ZN
Released
1 Mar 2023

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

Secondary structure: helices and β-sheets

7UIK contains 118 α-helices and 65 β-strands across 8 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 b: 2 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix29-5022
α-helix67-10337
Chain c: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix11-188
α-helix21-233
α-helix24-5532
α-helix64-9431
α-helix96-994
α-helix101-1099
Chain e: 43 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix288-30417
α-helix313-32412
α-helix335-35521
α-helix368-3758
α-helix376-3805
α-helix381-3866
α-helix393-4019
α-helix405-41814
α-helix439-44911
α-helix458-4614
β-strand479-48244
β-strand488-49144
α-helix494-50411
α-helix507-5093
α-helix521-5277
α-helix529-5313
α-helix534-55421
α-helix557-56913
α-helix574-5818
α-helix584-59714
α-helix600-6034
α-helix612-63625
α-helix641-6477
α-helix657-6637
α-helix683-69715
α-helix698-7025
α-helix707-7126
α-helix715-73521
α-helix742-7498
α-helix750-7523
α-helix757-7604
α-helix761-77616
α-helix781-79515
α-helix805-81410
α-helix816-8249
α-helix847-85812
α-helix868-8714
α-helix895-90814
α-helix917-92711
α-helix929-94618
α-helix959-97416
α-helix981-99111
α-helix1079-10824
α-helix1088-110518
α-helix1110-112920
Chain n: 6 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix835-84915
β-strand856-86052
β-strand864-86852
β-strand880-88672
β-strand891-89882
α-helix903-9075
α-helix908-9136
α-helix918-94225
β-strand956-96383
β-strand966-97383
β-strand978-991143
β-strand994-100293
α-helix1016-102510
β-strand105013
β-strand1054-105743
α-helix1059-107315
Chain o: 5 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix849-87527
α-helix880-89213
α-helix907-9148
α-helix920-9223
α-helix923-9319
β-strand938-93921
β-strand942-94321
Chain p: 42 helices, 51 β-strands
ElementResiduesLengthSheet
β-strand8-1035
β-strand16-1945
β-strand28-3145
β-strand33-3536
β-strand41-4336
α-helix44-463
β-strand47-4935
β-strand101-10227
β-strand105-11068
β-strand120-12568
β-strand130-13568
β-strand148-15478
β-strand159-16138
α-helix173-1742
β-strand178-17927
β-strand190-19569
β-strand197110
β-strand202-2111011
β-strand216-224911
β-strand230110
β-strand235-24399
β-strand247-25489
β-strand260-26679
α-helix273-2764
β-strand281-288812
β-strand294-301812
β-strand306-3151012
α-helix327-3293
β-strand330-3391012
α-helix340-3423
β-strand344113
β-strand350113
β-strand353-358614
β-strand371-377714
β-strand384-392914
β-strand426-4351014
β-strand439-444615
α-helix4451
β-strand450-455615
β-strand460-464515
β-strand470115
α-helix474-4774
β-strand485-488411
α-helix491-4933
β-strand497-498216
α-helix501-5033
α-helix504-5063
β-strand507-512617
β-strand518-523617
β-strand532-533217
β-strand534-535216
α-helix542-5443
α-helix545-56117
α-helix567-58317
α-helix585-60218
α-helix611-6188
α-helix623-63311
α-helix641-67535
α-helix683-72240
α-helix727-7293
α-helix731-7377
α-helix739-76123
α-helix768-7703
α-helix771-78212
α-helix788-80821
α-helix813-8164
α-helix817-8215
α-helix826-8283
α-helix829-84214
α-helix844-8463
α-helix849-8546
α-helix864-8663
β-strand868118
α-helix879-8813
β-strand88416
α-helix887-8893
α-helix892-8943
α-helix897-8993
β-strand901118
β-strand905119
β-strand912119
α-helix913-9142
α-helix915-9195
β-strand924-926320
β-strand932-933220
α-helix938-9403
α-helix941-9433
α-helix955-9595
β-strand962121
α-helix9671
β-strand968121
β-strand969-971320
α-helix972-9732
Chain T: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-113
α-helix12-132
α-helix14-185
α-helix29-335
α-helix51-7121
α-helix77-826
α-helix86-938
Chain U: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-113
α-helix12-176
α-helix29-346
α-helix41-455
α-helix51-7121
α-helix74-818
α-helix86-949

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA (38-mer)XDNA38Saccharomyces cerevisiae
DNA (37-mer)YDNA37Saccharomyces cerevisiae
Regulatory protein GAL4T, Uprotein147Saccharomyces cerevisiae S288CP04386 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 15oprotein1081Saccharomyces cerevisiae S288CP19659 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 2bprotein431Saccharomyces cerevisiae S288CQ12124 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 3cprotein397Saccharomyces cerevisiae S288CP40356 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 14nprotein241Saccharomyces cerevisiae S288CP19263
Mediator of RNA polymerase II transcription subunit 5eprotein1132Saccharomyces cerevisiae S288CP53114
Mediator of RNA polymerase II transcription subunit 16pprotein974Saccharomyces cerevisiae S288CP32259
Sequence of entity 1 (X), FASTA
>7UIK_1 DNA (38-MER) (chains X)
ACCGGAGGACAGTCCTCCCGACTGACTGACGTCGTACG
Sequence of entity 2 (Y), FASTA
>7UIK_2 DNA (37-MER) (chains Y)
CGTACGACGTCAGTCAGTCGGGAGGACTGTCCTCCGG
Sequence of entity 3 (T, U), FASTA
>7UIK_3 Regulatory protein GAL4 (chains T, U)
MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESR
LERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVTDRLASVETDMPL
TLRQHRISATSSSEESSNKGQRQLTVS
Sequence of entity 4 (o), FASTA
>7UIK_4 Mediator of RNA polymerase II transcription subunit 15 (chains o)
MSAAPVQDKDTLSNAERAKNVNGLLQVLMDINTLNGGSSDTADKIRIHAKNFEAALFAKS
SSKKEYMDSMNEKVAVMRNTYNTRKNAVTAAAANNNIKPVEQHHINNLKNSGNSANNMNV
NMNLNPQMFLNQQAQARQQVAQQLRNQQQQQQQQQQQQRRQLTPQQQQLVNQMKVAPIPK
QLLQRIPNIPPNINTWQQVTALAQQKLLTPQDMEAAKEVYKIHQQLLFKARLQQQQAQAQ
AQANNNNNGLPQNGNINNNINIPQQQQMQPPNSSANNNPLQQQSSQNTVPNVLNQINQIF
SPEEQRSLLQEAIETCKNFEKTQLGSTMTEPVKQSFIRKYINQKALRKIQALRDVKNNNN
ANNNGSNLQRAQNVPMNIIQQQQQQNTNNNDTIATSATPNAAAFSQQQNASSKLYQMQQQ
QQAQAQAQAQAQAQAQAQAQAQAAQAAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQ
AHAQHQPSQQPQQAQQQPNPLHGLTPTAKDVEVIKQLSLDASKTNLRLTDVTNSLSNEEK
EKIKMKLKQGQKLFVQVSNFAPQVYIITKNENFLKEVFQLRIFVKEILEKCAEGIFVVKL
DTVDRLIIKYQKYWESMRIQILRRQAILRQQQQMANNNGNPGTTSTGNNNNIATQQNMQQ
SLQQMQHLQQLKMQQQQQQQQQQQQQQQQQQQQQQQHIYPSSTPGVANYSAMANAPGNNI
PYMNHKNTSSMDFLNSMENTPKVPVSAAATPSLNKTINGKVNGRTKSNTIPVTSIPSTNK
KLSISNAASQQPTPRSASNTAKSTPNTNPSPLKTQTKNGTPNPNNMKTVQSPMGAQPSYN
SAIIENAFRKEELLLKDLEIRKLEISSRFKHRQEIFKDSPMDLFMSTLGDCLGIKDEEML
TSCTIPKAVVDHINGSGKRKPTKAAQRARDQDSIDISIKDNKLVMKSKFNKSNRSYSIAL
SNVAAIFKGIGGNFKDLSTLVHSSSPSTSSNMDVGNPRKRKASVLEISPQDSIASVLSPD
SNIMSDSKKIKVDSPDDPFMTKSGATTSEKQEVTNEAPFLTSGTSSEQFNVWDWNNWTSA
T
Sequence of entity 5 (b), FASTA
>7UIK_5 Mediator of RNA polymerase II transcription subunit 2 (chains b)
MVVQNSPVSSVHTANFSERGSNTRTMTYKNKLTVCFDDILKVGAEMMMQQQLKNVQLDSY
LVNGFSQSQQKLLKEKVKLFHGILDDLETSLSQSSSYLETLTALGKEKEKEREEAEKKRA
EQENMRKVREQEELKKRQELEEASQQQQLQQNSKEKNGLGLNFSTTAPANTTDANGSKEN
YQELGSLQSSSQTQLENANAANNGAAFSPLTTTRIQSQQAQPSDVMFNDLNSMDISMFSG
LDSTGFDSTAFNATVDETKGFDDNDSGNNYNDINISSIENNINNNINSTKNGKDNNNESN
KNNNGDEKNKNNNEDNENNNNSSEKNNNNNNNNNNNNDDNGNNNNNNSGNDNNNTTNNDS
NNKNNSITTGNDNENIVNNDLPTTVVSNPGDNPPPADNGEEYLTLNDFNDLNIDWSTTGD
NGELDLSGFNI
Sequence of entity 6 (c), FASTA
>7UIK_6 Mediator of RNA polymerase II transcription subunit 3 (chains c)
MDSIIPAGVKLDDLQVILAKNENETRDKVCKQINEARDEILPLRLQFNEFIQIMANIDQE
GSKQADRMAKYLHIRDKILQLNDRFQTLSSHLEALQPLFSTVPEYLKTADNRDRSFQLLE
PLSTYNKNGNAVCSTATVVSTNHSAAASTPTTTATPHANPITHAHSLSNPNSTATMQHNP
LAGKRGPKSGSTMGTPTVHNSTAAAPIAAPKKPRKPRQTKKAKAQAQAQAQAQAQVYAQQ
STVQTPITASMAAALPNPTPSMINSVSPTNVMGTPLTNMMSPMGNAYSMGAQNQGGQVSM
SQFNGSGNGSNPNTNTNSNNTPLQSQLNLNNLTPANILNMSMNNDFQQQQQQQQQQQQPQ
PQYNMNMGMNNMNNGGKELDSLDLNNLELGGLNMDFL
Sequence of entity 7 (n), FASTA
>7UIK_7 Mediator of RNA polymerase II transcription subunit 14 (chains n)
MQLVVLTDVVERLHKNFESENFKIIALQPNEISFKYLSNNDEDDKDCTIKISTNDDSIKN
LTVQLSPSNPQHIIQPFLDNSKMDYHFIFSYLQFTSSLFKALKVILNERGGKFHESGSQY
STMVNIGLHNLNEYQIVYYNPQAGTKITICIELKTVLHNGRDKIQFHIHFADVAHITTKS
PAYPMMHQVRNQVFMLDTKRLGTPESVKPANASHAIRLGNGVACDPSEIEPILMEIHNIL
K
Sequence of entity 8 (e), FASTA
>7UIK_8 Mediator of RNA polymerase II transcription subunit 5 (chains e)
MEKESVYNLALKCAERQLTSMEFSNLYKEFFNEKFPSLIQEEEEDTTTTANINEVKKASD
LVDTPSNNTAATADTTHLHEALDIVCSDFVKILNLEKPLILADYIVEVLLVNYNSDMIKC
FLPKLNSVRNSLLLAHFFSKSCSFFAKLSDTLIIDQVRKDLGNVIVPNILSLDMNSMNKE
LIAIVSKLLQTTLKLSPSPILLTSAGCKNGSFTLLNQLSQTNKLLFKRVSQTFEAKLHFK
DTKPFLNKDSTNEFVGSPSLTSPQYIPSPLSSTKPPGSVNSAAKYKDMKLLRYYKNIWLN
NKIINWEISNPDFLSKYSAITSSIFQESFNSVQNLDQLLTDLIETSFTCFAQFVSNKQYH
QANSNLTLLERKWVIFITKHLPLLILENSSRSPRVVTNALDNIDEKVVKAIRIYFTEKDD
NKTNNEDLFDDYPSTSLDIRHDFIKGLIMLNLQPASVINNYLREDQMIDTSILPTRDDLF
VRNLQGIQEVVHNTNSFIISSLDTLELESITESITHDSSNGLFQVLHNFESVAPTKQREI
VKAFLSIFEDAIKELNYNRIAKICALLFFNFSHSLTTILSFSSPAALMKTLIKFVDLSRN
GRNGSNGNDESSEYETINISLSFSWAILLIINLTQTYGISVVDVALKYPELSIKNSFIIN
FISNLPNVSDKYYLEESNVNDSDMLTKSHNTVQSWLCDLFVNGSITDQLIQNIETRQLAN
LIPFIVKQVLLSVEIGVLTDISSLIGGFEYFLQPLLLVGLIKTFYWLEQFLSCVKNDTIS
EDILQGIFNLLNTLFNPVTLNEDSKAFHTAVLRLNAIPLLKVLRKFRVQSQSNYGIYSSD
AQGDPNLEPLIAKLVAVLNVSPVYDVDPRIINSENDYSRKQLGYGKFLILNENPINKIMT
NQINSFWSLHSSTYYNLDYLFELIELVTPKSFLFDVLKTLEYKLATYGVPGSENKRGSLD
SEHVFDYFFYFLVLYDVKTAEEASQLIEYMENDAKKSKGDVDIKGEDLHEKNDSAEVRQE
TQPKAEATQDDDFDMLFGENDTSTQAYEEEEENEDNDGNNRTNNVPMIKAEETPSKTNKI
SILKRHSFAVLLHERKLLNDLALENGEITKTENEKFISYHDKYLCMLKTCVF
Sequence of entity 9 (p), FASTA
>7UIK_9 Mediator of RNA polymerase II transcription subunit 16 (chains p)
MMLGEHLMSWSKTGIIAYSDSQSSNANICLTFLESINGINWRFHTPQKYVLHPQLHEVQY
QESSSTLSTHSTTTSVNGSTTAGVGSTPNFGGNSNKSPPQFFYNISSIHWNNWFSLPGDM
LAVCDELGNMTMLITGQRPDRATTYEKLTMVFQDNVYKIYNHVMPLKPVDKLKPMNIERK
QTRKEYNTSILEFRWLTSSKSVIVSQFCAFDSSSNTYRSRAQQVPPYGVYHPPFIKYACL
AIRKNGQIDFWYQFSNSKDHKKITLQLLDTSNQRFKDLQWLEFARITPMNDDQCMLITTY
SKLSKNISFYKLHVNWNLNATKPNVLNDPSLKIQFILSTTLDPTDDEGHVLKLENLHVVS
KSSIEKDPSPEILVLYNVCDTSKSLVKRYRLAPTQLSAEYLVILKPDLNIDRNNSTNQIF
QSRRYNLRRHSDIVLDKKVTLITSEMFDAFVSFYFEDGTIESYNQNDWKLETERLISQSQ
LGKFKNIIASPLSAGFNYGKLPLPPSVEWMKVSPSMCGVIVKQYNKKWPQFYAAVQKNYA
DPEKDSINATALAFGYVKSLHKQISAEDLTIAAKTHILRISFLDRKRAKEFITTLLKSLY
SFFNISPDAPKEIMDKIITSRPLQKIMLLQLELGSCFSQENIEEMARVILYLKNVLFAFN
GVARNFHFAIEQISNNSNQQQNPKLFQTIFSKQDLIHSLIPVAKWFVKFITYLTQEILIL
INDPTNKEYTLVHGIFGAKMSRTLILSILNEIKKVTQIVAKFPETSYPILNESSTFLKLV
LSESPVDFEKFETFLVDVNNKFIALCEQQPSQEREFSLLVKAEIPPEYAKVGDFLLQYAN
NAVISHANAAAVYFADTSGLKISNSEFFNPEIFHLLQPLEEGLIIDTDKLPIKNRTSKSF
SKLLYDDVTCDKLSVSEISDGKLKRCSRCGSVTRAGNIISSDKTIVPTSIQTKRWPTMYT
RLCICSGMLFEMDG

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn4

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 P04386 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 7UIK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.