8T9D: TR-TRAP

CryoEM structure of TR-TRAP. Determined by electron microscopy at 4.66 Å resolution. Released 3 Jul 2024.

Method
Electron microscopy
Resolution
4.66 Å
Organism
Homo sapiens
Chains
26
Atoms
49,136
Mol. weight
1529.69 kDa
Released
3 Jul 2024

Explore 8T9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T9D contains 323 α-helices and 116 β-strands across 25 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 a: 1 helix, 0 β-strands

ElementResiduesLengthSheet
α-helix6-1712
Chain A: 16 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix23-253
α-helix61-644
α-helix66-694
α-helix74-8411
α-helix85-895
α-helix136-1383
α-helix153-1608
α-helix172-1809
α-helix183-19412
β-strand21511
β-strand21811
β-strand25612
β-strand30612
α-helix315-3217
α-helix339-34810
β-strand36613
β-strand37113
α-helix409-42113
α-helix422-4243
β-strand449-45134
β-strand45415
β-strand46315
β-strand466-46834
β-strand476-47724
α-helix492-50110
α-helix504-5107
α-helix511-5155
Chain B: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix28-5124
α-helix64-14077
α-helix145-15612
α-helix180-1834
Chain C: 8 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix28-347
α-helix47-515
α-helix58-625
β-strand68-7036
β-strand81-8336
α-helix101-1033
α-helix111-13424
α-helix176-1816
α-helix184-1874
α-helix190-1923
Chain D: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix20-245
α-helix74-9724
α-helix104-17471
Chain E: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix4-3532
α-helix42-6221
α-helix118-1236
α-helix175-18612
Chain F: 3 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix66-7712
α-helix87-10317
α-helix111-13727
Chain G: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix8-2619
α-helix37-5923
α-helix65-739
α-helix78-11639
α-helix118-1225
α-helix123-1275

17 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Mediator of RNA polymerase II transcription subunit 1Aprotein1581Homo sapiensQ15648 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 4Bprotein270Homo sapiensQ9NPJ6 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 6Cprotein246Homo sapiensO75586 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 7Dprotein233Homo sapiensO43513 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 8Eprotein268Homo sapiensQ96G25
Mediator of RNA polymerase II transcription subunit 9Fprotein146Homo sapiensQ9NWA0
Mediator of RNA polymerase II transcription subunit 10Gprotein135Homo sapiensQ9BTT4
Mediator of RNA polymerase II transcription subunit 11Hprotein117Homo sapiensQ9P086
Mediator of RNA polymerase II transcription subunit 14Iprotein1454Homo sapiensO60244
Mediator of RNA polymerase II transcription subunit 15Jprotein788Homo sapiensQ96RN5
Mediator of RNA polymerase II transcription subunit 16Kprotein877Homo sapiensQ9Y2X0
Mediator of RNA polymerase II transcription subunit 17Lprotein651Homo sapiensQ9NVC6

14 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>8T9D_1 Mediator of RNA polymerase II transcription subunit 1 (chains A)
MKAQGETEESEKLSKMSSLLERLHAKFNQNRPWSETIKLVRQVMEKRVVMSSGGHQHLVS
CLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPAGQL
CDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSL
EQDLSKMAIMYWKATNAGPLDKILHGSVGYLTPRSGGHLMNLKYYVSPSDLLDDKTASPI
ILHENNVSRSLGMNASVTIEGTSAVYKLPIAPLIMGSHPVDNKWTPSFSSITSANSVDLP
ACFFLKFPQPIPVSRAFVQKLQNCTGIPLFETQPTYAPLYELITQFELSKDPDPIPLNHN
MRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLVSKITFQHPGRVPLILNLIRHQVAYNTL
IGSCVKRTILKEDSPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTHVSCKLY
KGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNL
PPASSPGYGMTTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQ
NPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTL
YGSSPLERQNSSSGSPRMEICSGSNKTKKKKSSRLPPEKPKHQTEDDFQRELFSMDVDSQ
NPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQPVPHPQPSIQRMVRLSSSDSIGPDVT
DILSDIAEEASKLPSTSDDCPAIGTPLRDSSSSGHSQSTLFDSDVFQTNNNENPYTDPAD
LIADAAGSPSSDSPTNHFFHDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFAS
QALNTLGVPMLGGDNGETKFKGNNQADTVDFSIISVAGKALAPADLMEHHSGSQGPLLTT
GDLGKEKTQKRVKEGNGTSNSTLSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKADTEGK
SPSHSSSNRPFTPPTSTGGSKSPGSAGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSSH
SQYTSSGSVSSSGSKSHHSHSSSSSSSASTSGKMKSSKSEGSSSSKLSSSMYSSQGSSGS
SQSKNSSQSGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPSLSKPNISPSHSRPPG
GSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSGTSSSSGMKSSSGLGSSGSLSQKTP
PSSNSCTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPG
GEDPLDGQMGVSTNSSSHPMSSKHNMSGGEFQGKREKSDKDKSKVSTSGSSVDSSKKTSE
SKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMASSKNYGSPLISGST
PKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKH
KKEKKKVKDKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSMTSNTILSADRPSRL
SPDFMIGEEDDDLMDVALIGN
Sequence of entity 2 (B), FASTA
>8T9D_2 Mediator of RNA polymerase II transcription subunit 4 (chains B)
MAASSSGEKEKERLGGGLGVAGGNSTRERLLSALEDLEVLSRELIEMLAISRNQKLLQAG
EENQVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQI
LATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDL
EMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDF
LLEPPGHNKENEDDVEIMSTDSSSSSSESD
Sequence of entity 3 (C), FASTA
>8T9D_3 Mediator of RNA polymerase II transcription subunit 6 (chains C)
MAAVDIRDNLLGISWVDSSWIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHL
NQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVL
TAVHGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDAL
LLDLRQKFPPKFVQLKPGEKPVPVDQTKKEAEPIPETVKPEEKETTKNVQQTVSAKGPPE
KRMRLQ
Sequence of entity 4 (D), FASTA
>8T9D_4 Mediator of RNA polymerase II transcription subunit 7 (chains D)
MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
SQGIERLHPMQFDHKKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
Sequence of entity 5 (E), FASTA
>8T9D_5 Mediator of RNA polymerase II transcription subunit 8 (chains E)
MQREEKQLEASLDALLSQVADLKNSLGSFICKLENEYGRLTWPSVLDSFALLSGQLNTLN
KVLKHEKTPLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQ
EKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTNA
LVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGVQ
MAQAGQPGKMPSGIKTNIKSASMHPYQR
Sequence of entity 6 (F), FASTA
>8T9D_6 Mediator of RNA polymerase II transcription subunit 9 (chains F)
MASAGVAAGRQAEDVLPPTSDQPLPDTKPLPPPQPPPVPAPQPQQSPAPRPQSPARAREE
ENYSFLPLVHNIIKCMDKDSPEVHQDLNALKSKFQEMRKLISTMPGIHLSPEQQQQQLQS
LREQVRTKNELLQKYKSLCMFEIPKE
Sequence of entity 7 (G), FASTA
>8T9D_7 Mediator of RNA polymerase II transcription subunit 10 (chains G)
MAEKFDHLEEHLEKFVENIRQLGIIVSDFQPSSQAGLNQKLNFIVTGLQDIDKCRQQLHD
ITVPLEVFEYIDQGRNPQLYTKECLERALAKNEQVKGKIDTMKKFKSLLIQELSKVFPED
MAKYRSIRGEDHPPS
Sequence of entity 8 (H), FASTA
>8T9D_8 Mediator of RNA polymerase II transcription subunit 11 (chains H)
MATYSLANERLRALEDIEREIGAILQNAGTVILELSKEKTNERLLDRQAAAFTASVQHVE
AELSAQIRYLTQVATGQPHEGSSYSSRKDCQMALKRVDYARLKLSDVARTCEQMLEN
Sequence of entity 9 (I), FASTA
>8T9D_9 Mediator of RNA polymerase II transcription subunit 14 (chains I)
MAPVQLENHQLVPPGGGGGGSGGPPSAPAPPPPGAAVAAAAAAAASPGYRLSTLIEFLLH
RAYSELMVLTDLLPRKSDVERKIEIVQFASRTRQLFVRLLALVKWANNAGKVEKCAMISS
FLDQQAILFVDTADRLASLARDALVHARLPSFAIPYAIDVLTTGSYPRLPTCIRDKIIPP
DPITKIEKQATLHQLNQILRHRLVTTDLPPQLANLTVANGRVKFRVEGEFEATLTVMGDD
PDVPWRLLKLEILVEDKETGDGRALVHSMQISFIHQLVQSRLFADEKPLQDMYNCLHSFC
LSLQLEVLHSQTLMLIRERWGDLVQVERYHAGKCLSLSVWNQQVLGRKTGTASVHKVTIK
IDENDVSKPLQIFHDPPLPASDSKLVERAMKIDHLSIEKLLIDSVHARAHQKLQELKAIL
RGFNANENSSIETALPALVVPILEPCGNSECLHIFVDLHSGMFQLMLYGLDQATLDDMEK
SVNDDMKRIIPWIQQLKFWLGQQRCKQSIKHLPTISSETLQLSNYSTHPIGNLSKNKLFI
KLTRLPQYYIVVEMLEVPNKPTQLSYKYYFMSVNAADREDSPAMALLLQQFKENIQDLVF
RTKTGKQTRTNAKRKLSDDPCPVESKKTKRAGEMCAFNKVLAHFVAMCDTNMPFVGLRLE
LSNLEIPHQGVQVEGDGFSHAIRLLKIPPCKGITEETQKALDRSLLDCTFRLQGRNNRTW
VAELVFANCPLNGTSTREQGPSRHVYLTYENLLSEPVGGRKVVEMFLNDWNSIARLYECV
LEFARSLPDIPAHLNIFSEVRVYNYRKLILCYGTTKGSSISIQWNSIHQKFHISLGTVGP
NSGCSNCHNTILHQLQEMFNKTPNVVQLLQVLFDTQAPLNAINKLPTVPMLGLTQRTNTA
YQCFSILPQSSTHIRLAFRNMYCIDIYCRSRGVVAIRDGAYSLFDNSKLVEGFYPAPGLK
TFLNMFVDSNQDARRRSVNEDDNPPSPIGGDMMDSLISQLQPPPQQQPFPKQPGTSGAYP
LTSPPTSYHSTVNQSPSMMHTQSPGNLHAASSPSGALRAPSPASFVPTPPPSSHGISIGP
GASFASPHGTLDPSSPYTMVSPSGRAGNWPGSPQVSGPSPAARMPGMSPANPSLHSPVPD
ASHSPRAGTSSQTMPTNMPPPRKLPQRSWAASIPTILTHSALNILLLPSPTPGLVPGLAG
SYLCSPLERFLGSVIMRRHLQRIIQQETLQLINSNEPGVIMFKTDALKCRVALSPKTNQT
LQLKVTPENAGQWKPDELQVLEKFFETRVAGPPFKANTLIAFTKLLGAPTHILRDCVHIM
KLELFPDQATQLKWNVQFCLTIPPSAPPIAPPGTPAVVLKSKMLFFLQLTQKTSVPPQEP
VSIIVPIIYDMASGTTQQADIPRQQNSSVAAPMMVSNILKRFAEMNPPRQGECTIFAAVR
DLMANLTLPPGGRP
Sequence of entity 10 (J), FASTA
>8T9D_10 Mediator of RNA polymerase II transcription subunit 15 (chains J)
MDVSGQETDWRSTAFRQKLVSQIEDAMRKAGVAHSKSSKDMESHVFLKAKTRDEYLSLVA
RLIIHFRDIHNKKSQASVSDPMNALQSLTGGPAAGAAGIGMPPRGPGQSLGGMGSLGAMG
QPMSLSGQPPPGTSGMAPHSMAVVSTATPQTQLQLQQVALQQQQQQQQFQQQQQAALQQQ
QQQQQQQQFQAQQSAMQQQFQAVVQQQQQLQQQQQQQQHLIKLHHQNQQQIQQQQQQLQR
IAQLQLQQQQQQQQQQQQQQQQALQAQPPIQQPPMQQPQPPPSQALPQQLQQMHHTQHHQ
PPPQPQQPPVAQNQPSQLPPQSQTQPLVSQAQALPGQMLYTQPPLKFVRAPMVVQQPPVQ
PQVQQQQTAVQTAQAAQMVAPGVQMITEALAQGGMHIRARFPPTTAVSAIPSSSIPLGRQ
PMAQVSQSSLPMLSSPSPGQQVQTPQSMPPPPQPSPQPGQPSSQPNSNVSSGPAPSPSSF
LPSPSPQPSQSPVTARTPQNFSVPSPGPLNTPVNPSSVMSPAGSSQAEEQQYLDKLKQLS
KYIEPLRRMINKIDKNEDRKKDLSKMKSLLDILTDPSKRCPLKTLQKCEIALEKLKNDMA
VPTPPPPPVPPTKQQYLCQPLLDAVLANIRSPVFNHSLYRTFVPAMTAIHGPPITAPVVC
TRKRRLEDDERQSIPSVLQGEVARLDPKFLVNLDPSHCSNNGTVHLICKLDDKDLPSVPP
LELSVPADYPAQSPLWIDRQWQYDANPFLQSVHRCMTSRLLQLPDKHSVTALLNTWAQSV
HQACLSAA
Sequence of entity 11 (K), FASTA
>8T9D_11 Mediator of RNA polymerase II transcription subunit 16 (chains K)
MCDLRRPAAGGMMDLAYVCEWEKWSKSTHCPSVPLACAWSCRNLIAFTMDLRSDDQDLTR
MIHILDTEHPWDLHSIPSEHHEAITCLEWDQSGSRLLSADADGQIKCWSMADHLANSWES
SVGSLVEGDPIVALSWLHNGVKLALHVEKSGASSFGEKFSRVKFSPSLTLFGGKPMEGWI
AVTVSGLVTVSLLKPSGQVLTSTESLCRLRGRVALADIAFTGGGNIVVATADGSSASPVQ
FYKVCVSVVSEKCRIDTEILPSLFMRCTTDLNRKDKFPAITHLKFLARDMSEQVLLCASS
QTSSIVECWSLRKEGLPVNNIFQQISPVVGDKQPTILKWRILSATNDLDRVSAVALPKLP
ISLTNTDLKVASDTQFYPGLGLALAFHDGSVHIVHRLSLQTMAVFYSSAAPRPVDEPAMK
RPRTAGPAVHLKAMQLSWTSLALVGIDSHGKLSVLRLSPSMGHPLEVGLALRHLLFLLEY
CMVTGYDWWDILLHVQPSMVQSLVEKLHEEYTRQTAALQQVLSTRILAMKASLCKLSPCT
VTRVCDYHTKLFLIAISSTLKSLLRPHFLNTPDKSPGDRLTEICTKITDVDIDKVMINLK
TEEFVLDMNTLQALQQLLQWVGDFVLYLLASLPNQGSLLRPGHSFLRDGTSLGMLRELMV
VIRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWICCRDEGPASEPDEALVDECCLL
PSQLLIPSLDWLPASDGLVSRLQPKQPLRLQFGRAPTLPGSAATLQLDGLARAPGQPKID
HLRRLHLGACPTEECKACTRCGCVTMLKSPNRTTAVKQWEQRWIKNCLAVEGRGPDACVT
SRASEEAPAFVQLGPQSTHHSPRTPRSLDHLHPEDRP
Sequence of entity 12 (L), FASTA
>8T9D_12 Mediator of RNA polymerase II transcription subunit 17 (chains L)
MSGVRAVRISIESACEKQVHEVGLDGTETYLPPLSMSQNLARLAQRIDFSQGSGSEEEEA
AGTEGDAQEWPGAGSSADQDDEEGVVKFQPSLWPWDSVRNNLRSALTEMCVLYDVLSIVR
DKKFMTLDPVSQDALPPKQNPQTLQLISKKKSLAGAAQILLKGAERLTKSVTENQENKLQ
RDFNSELLRLRQHWKLRKVGDKILGDLSYRSAGSLFPHHGTFEVIKNTDLDLDKKIPEDY
CPLDVQIPSDLEGSAYIKVSIQKQAPDIGDLGTVNLFKRPLPKSKPGSPHWQTKLEAAQN
VLLCKEIFAQLSREAVQIKSQVPHIVVKNQIISQPFPSLQLSISLCHSSNDKKSQKFATE
KQCPEDHLYVLEHNLHLLIREFHKQTLSSIMMPHPASAPFGHKRMRLSGPQAFDKNEINS
LQSSEGLLEKIIKQAKHIFLRSRAAATIDSLASRIEDPQIQAHWSNINDVYESSVKVLIT
SQGYEQICKSIQLQLNIGVEQIRVVHRDGRVITLSYQEQELQDFLLSQMSQHQVHAVQQL
AKVMGWQVLSFSNHVGLGPIESIGNASAITVASPSGDYAISVRNGPESGSKIMVQFPRNQ
CKDLPKSDVLQDNKWSHLRGPFKEVQWNKMEGRNFVYKMELLMSALSPCLL

Primary citation

An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Zhao, H., Li, J., Xiang, Y. et al. Mol Cell (2024) 84:2648-2664.e10. DOI 10.1016/j.molcel.2024.06.006 · PubMed

Other PDB entries of the same protein (UniProt Q15648 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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