7EMF: PDB entry 7EMF
Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation. Determined by electron microscopy at 3.5 Å resolution. Released 5 May 2021.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 27
- Atoms
- 62,334
- Mol. weight
- 1378.1 kDa
- Ligands
- ZN
- Released
- 5 May 2021
Explore 7EMF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7EMF contains 362 α-helices and 202 β-strands across 27 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: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-37 | 30 | |
| α-helix | 45-76 | 32 | |
| α-helix | 104-130 | 27 | |
| α-helix | 159-171 | 13 | |
| β-strand | 176-181 | 6 | 54 |
| β-strand | 189-194 | 6 | 54 |
| β-strand | 198-204 | 7 | 54 |
| β-strand | 209-216 | 8 | 54 |
| β-strand | 222 | 1 | 55 |
| β-strand | 228 | 1 | 55 |
| α-helix | 237-252 | 16 | |
| α-helix | 260-271 | 12 | |
| α-helix | 272-275 | 4 | |
| α-helix | 279-281 | 3 | |
| β-strand | 296-297 | 2 | 56 |
| β-strand | 304-305 | 2 | 56 |
| α-helix | 307-309 | 3 | |
Chain 1: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-55 | 12 | |
| α-helix | 70-105 | 36 | |
| α-helix | 108-143 | 36 | |
Chain 2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-89 | 34 | |
| α-helix | 102-135 | 34 | |
| α-helix | 157-185 | 29 | |
Chain 3: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-57 | 28 | |
| α-helix | 70-101 | 32 | |
| β-strand | 117 | 1 | 45 |
| α-helix | 137-175 | 39 | |
Chain 4: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-28 | 18 | |
| α-helix | 31-39 | 9 | |
| α-helix | 46-54 | 9 | |
| α-helix | 55-59 | 5 | |
| α-helix | 61-64 | 4 | |
| α-helix | 72-79 | 8 | |
| α-helix | 83-86 | 4 | |
| α-helix | 91-105 | 15 | |
| α-helix | 107-121 | 15 | |
Chain A: 19 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-26 | 13 | |
| α-helix | 34-45 | 12 | |
| α-helix | 57-66 | 10 | |
| α-helix | 67-69 | 3 | |
| α-helix | 74-88 | 15 | |
| α-helix | 90 | 1 | |
| β-strand | 91-94 | 4 | 1 |
| β-strand | 100-103 | 4 | 1 |
| β-strand | 108-111 | 4 | 1 |
| α-helix | 136-143 | 8 | |
| α-helix | 147-160 | 14 | |
| α-helix | 168-194 | 27 | |
| α-helix | 199-204 | 6 | |
| β-strand | 210-212 | 3 | 2 |
| α-helix | 213-214 | 2 | |
| β-strand | 215 | 1 | 3 |
| β-strand | 218 | 1 | 3 |
| β-strand | 220-225 | 6 | 2 |
| α-helix | 228-231 | 4 | |
| β-strand | 253-261 | 9 | 2 |
| β-strand | 268-269 | 2 | 4 |
| β-strand | 296-297 | 2 | 4 |
| β-strand | 301-314 | 14 | 2 |
| α-helix | 315-325 | 11 | |
| β-strand | 337-338 | 2 | 2 |
| α-helix | 339-348 | 10 | |
| β-strand | 362-366 | 5 | 5 |
| β-strand | 371-375 | 5 | 5 |
| α-helix | 380-382 | 3 | |
| β-strand | 389-398 | 10 | 2 |
| α-helix | 401-403 | 3 | |
| α-helix | 404-422 | 19 | |
| β-strand | 438-446 | 9 | 5 |
| β-strand | 449-455 | 7 | 5 |
| β-strand | 462-469 | 8 | 5 |
| β-strand | 475-480 | 6 | 5 |
| α-helix | 491-501 | 11 | |
| α-helix | 504-517 | 14 | |
Chain B: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-17 | 12 | |
Chain D: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-51 | 25 | |
| α-helix | 63-140 | 78 | |
| β-strand | 143-144 | 2 | 6 |
| α-helix | 145-156 | 12 | |
| α-helix | 179-183 | 5 | |
| α-helix | 186-189 | 4 | |
19 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 |
|---|
| Mediator of RNA polymerase II transcription subunit 1 | A | protein | 1581 | Homo sapiens | Q15648 (AlphaFold model) |
| Unknown Chain (poly A) | B | protein | 20 | Homo sapiens | |
| Mediator of RNA polymerase II transcription subunit 4 | D | protein | 270 | Homo sapiens | Q9NPJ6 (AlphaFold model) |
| Mediator of RNA polymerase II transcription subunit 6 | F | protein | 246 | Homo sapiens | O75586 (AlphaFold model) |
| Mediator of RNA polymerase II transcription subunit 7 | G | protein | 233 | Homo sapiens | O43513 (AlphaFold model) |
| Isoform 2 of Mediator of RNA polymerase II transcription subunit 8 | H | protein | 268 | Homo sapiens | Q96G25 |
| Mediator of RNA polymerase II transcription subunit 9 | I | protein | 146 | Homo sapiens | Q9NWA0 |
| Mediator of RNA polymerase II transcription subunit 10 | J | protein | 135 | Homo sapiens | Q9BTT4 |
| Mediator of RNA polymerase II transcription subunit 11 | K | protein | 117 | Homo sapiens | Q9P086 |
| Mediator of RNA polymerase II transcription subunit 14 | N | protein | 1454 | Homo sapiens | O60244 |
| Mediator of RNA polymerase II transcription subunit 15 | O | protein | 788 | Homo sapiens | Q96RN5 |
| Isoform 2 of Mediator of RNA polymerase II transcription subunit 16 | P | protein | 841 | Homo sapiens | Q9Y2X0 |
15 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>7EMF_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
>7EMF_2 Unknown Chain (poly A) (chains B)
AAAAAAAAAAAAAAAAAAAA
Sequence of entity 3 (D), FASTA
>7EMF_3 Mediator of RNA polymerase II transcription subunit 4 (chains D)
MAASSSGEKEKERLGGGLGVAGGNSTRERLLSALEDLEVLSRELIEMLAISRNQKLLQAG
EENQVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQI
LATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDL
EMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDF
LLEPPGHNKENEDDVEIMSTDSSSSSSESD
Sequence of entity 4 (F), FASTA
>7EMF_4 Mediator of RNA polymerase II transcription subunit 6 (chains F)
MAAVDIRDNLLGISWVDSSWIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHL
NQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVL
TAVHGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDAL
LLDLRQKFPPKFVQLKPGEKPVPVDQTKKEAEPIPETVKPEEKETTKNVQQTVSAKGPPE
KRMRLQ
Sequence of entity 5 (G), FASTA
>7EMF_5 Mediator of RNA polymerase II transcription subunit 7 (chains G)
MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
SQGIERLHPMQFDHKKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
Sequence of entity 6 (H), FASTA
>7EMF_6 Isoform 2 of Mediator of RNA polymerase II transcription subunit 8 (chains H)
MQREEKQLEASLDALLSQVADLKNSLGSFICKLENEYGRLTWPSVLDSFALLSGQLNTLN
KVLKHEKTPLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQ
EKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTNA
LVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGVQ
MAQAGQPGKMPSGIKTNIKSASMHPYQR
Sequence of entity 7 (I), FASTA
>7EMF_7 Mediator of RNA polymerase II transcription subunit 9 (chains I)
MASAGVAAGRQAEDVLPPTSDQPLPDTKPLPPPQPPPVPAPQPQQSPAPRPQSPARAREE
ENYSFLPLVHNIIKCMDKDSPEVHQDLNALKSKFQEMRKLISTMPGIHLSPEQQQQQLQS
LREQVRTKNELLQKYKSLCMFEIPKE
Sequence of entity 8 (J), FASTA
>7EMF_8 Mediator of RNA polymerase II transcription subunit 10 (chains J)
MAEKFDHLEEHLEKFVENIRQLGIIVSDFQPSSQAGLNQKLNFIVTGLQDIDKCRQQLHD
ITVPLEVFEYIDQGRNPQLYTKECLERALAKNEQVKGKIDTMKKFKSLLIQELSKVFPED
MAKYRSIRGEDHPPS
Sequence of entity 9 (K), FASTA
>7EMF_9 Mediator of RNA polymerase II transcription subunit 11 (chains K)
MATYSLANERLRALEDIEREIGAILQNAGTVILELSKEKTNERLLDRQAAAFTASVQHVE
AELSAQIRYLTQVATGQPHEGSSYSSRKDCQMALKRVDYARLKLSDVARTCEQMLEN
Sequence of entity 10 (N), FASTA
>7EMF_10 Mediator of RNA polymerase II transcription subunit 14 (chains N)
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 11 (O), FASTA
>7EMF_11 Mediator of RNA polymerase II transcription subunit 15 (chains O)
MDVSGQETDWRSTAFRQKLVSQIEDAMRKAGVAHSKSSKDMESHVFLKAKTRDEYLSLVA
RLIIHFRDIHNKKSQASVSDPMNALQSLTGGPAAGAAGIGMPPRGPGQSLGGMGSLGAMG
QPMSLSGQPPPGTSGMAPHSMAVVSTATPQTQLQLQQVALQQQQQQQQFQQQQQAALQQQ
QQQQQQQQFQAQQSAMQQQFQAVVQQQQQLQQQQQQQQHLIKLHHQNQQQIQQQQQQLQR
IAQLQLQQQQQQQQQQQQQQQQALQAQPPIQQPPMQQPQPPPSQALPQQLQQMHHTQHHQ
PPPQPQQPPVAQNQPSQLPPQSQTQPLVSQAQALPGQMLYTQPPLKFVRAPMVVQQPPVQ
PQVQQQQTAVQTAQAAQMVAPGVQMITEALAQGGMHIRARFPPTTAVSAIPSSSIPLGRQ
PMAQVSQSSLPMLSSPSPGQQVQTPQSMPPPPQPSPQPGQPSSQPNSNVSSGPAPSPSSF
LPSPSPQPSQSPVTARTPQNFSVPSPGPLNTPVNPSSVMSPAGSSQAEEQQYLDKLKQLS
KYIEPLRRMINKIDKNEDRKKDLSKMKSLLDILTDPSKRCPLKTLQKCEIALEKLKNDMA
VPTPPPPPVPPTKQQYLCQPLLDAVLANIRSPVFNHSLYRTFVPAMTAIHGPPITAPVVC
TRKRRLEDDERQSIPSVLQGEVARLDPKFLVNLDPSHCSNNGTVHLICKLDDKDLPSVPP
LELSVPADYPAQSPLWIDRQWQYDANPFLQSVHRCMTSRLLQLPDKHSVTALLNTWAQSV
HQACLSAA
Sequence of entity 12 (P), FASTA
>7EMF_12 Isoform 2 of Mediator of RNA polymerase II transcription subunit 16 (chains P)
MCDLRRPAAGGMMDLAYVCEWEKWSKSTHCPSVPLACAWSCRNLIAFTMDLRSDDQDLTR
MIHILDTEHPWDLHSIPSEHHEAITCLEWDQSGSRLLSADADGQIKCWSMADHLANSWES
SVGSLVEGDPIVALSWLHNGVKLALHVEKSGASSFGEKFSRVKFSPSLTLFGGKPMEGWI
AVTVSGLVTVSLLKPSGQVLTSTESLCRLRGRVALADIAFTGGGNIVVATADGSSASPVQ
FYKVCVSVVSEKCRIDTEILPSLFMRCTTDLNRKDKFPAITHLKFLARDMSEQVLLCASS
QTSSIVECWSLRKEGLPVNNIFQQISPVVGDKQPTILKWRILSATNDLDRVSAVALPKLP
ISLTNTDLKVASDTQFYPGLGLALAFHDGSVHIVHRLSLQTMAVFYSSAAPRPVDEPAMK
RPRTAGPAVHLKAMQLSWTSLALVGIDSHGKLSVLRLSPSMGHPLEVGLALRHLLFLLEY
CMVTGYDWWDILLHVQPSMVQSLVEKLHEEYTRQTAALQQVLSTRILAMKASLCKLSPCT
VTRVCDYHTKLFLIAISSTLKSLLRPHFLNTPDKSPGDRLTEICTKITDVDIDKVMINLK
TEEFVLDMNTLQALQQLLQWVGDFVLYLLASLPNQGSLLRPGHSFLRDGTSLGMLRELMV
VIRIWGLLKPSCLPVYTATSDTQDSMSLLFRLLTKLWICCRDEGPASEPDEALVDECCLL
PSQLLIPSLDWLPASDGLVSRLQPKQPLRLQFGRAPTLPGSAATLQLDGLARAPGQPKID
HLRRLHLGACPTEECKACTRCGCVTMLKSPNRTTAVKQWEQRWIKNCLCGGLWWRVPLSY
P
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structures of the human Mediator and Mediator-bound preinitiation complex. Chen, X., Yin, X., Li, J. et al. Science (2021) 372. DOI 10.1126/science.abg0635 · PubMed
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