8TRH: The IDRc bound human core Mediator complex
The IDRc bound human core Mediator complex. Determined by electron microscopy at 3.7 Å resolution. Released 9 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Homo sapiens
- Chains
- 26
- Atoms
- 59,957
- Mol. weight
- 1477.91 kDa
- Ligands
- ZN
- Released
- 9 Oct 2024
Explore 8TRH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8TRH contains 330 α-helices and 175 β-strands across 26 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: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-37 | 29 | |
| α-helix | 45-76 | 32 | |
| α-helix | 104-128 | 25 | |
| α-helix | 159-171 | 13 | |
| β-strand | 176-181 | 6 | 1 |
| β-strand | 188-194 | 7 | 1 |
| β-strand | 198-205 | 8 | 1 |
| β-strand | 208-215 | 8 | 1 |
| β-strand | 222 | 1 | 2 |
| β-strand | 228 | 1 | 2 |
| α-helix | 237-252 | 16 | |
| α-helix | 260-271 | 12 | |
| α-helix | 272-275 | 4 | |
| β-strand | 289 | 1 | 3 |
| β-strand | 292 | 1 | 3 |
| β-strand | 296-297 | 2 | 4 |
| β-strand | 304-305 | 2 | 4 |
Chain 1: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-55 | 12 | |
| α-helix | 71-105 | 35 | |
| α-helix | 108-144 | 37 | |
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, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-57 | 28 | |
| α-helix | 71-101 | 31 | |
| α-helix | 137-175 | 39 | |
Chain 4: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-27 | 17 | |
| α-helix | 31-40 | 10 | |
| α-helix | 47-54 | 8 | |
| α-helix | 55-59 | 5 | |
| α-helix | 61-65 | 5 | |
| α-helix | 71-79 | 9 | |
| α-helix | 92-114 | 23 | |
Chain A: 17 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-25 | 12 | |
| α-helix | 34-45 | 12 | |
| α-helix | 57-66 | 10 | |
| α-helix | 70-71 | 2 | |
| α-helix | 74-88 | 15 | |
| β-strand | 91-94 | 4 | 5 |
| β-strand | 100-103 | 4 | 5 |
| β-strand | 108-111 | 4 | 5 |
| α-helix | 136-143 | 8 | |
| α-helix | 147-159 | 13 | |
| α-helix | 169-194 | 26 | |
| α-helix | 199-203 | 5 | |
| β-strand | 210-212 | 3 | 6 |
| β-strand | 215 | 1 | 7 |
| β-strand | 218 | 1 | 7 |
| α-helix | 219-220 | 2 | |
| β-strand | 221-225 | 5 | 6 |
| α-helix | 228-231 | 4 | |
| β-strand | 253-269 | 17 | 6 |
| β-strand | 277-278 | 2 | 8 |
| β-strand | 281-282 | 2 | 8 |
| α-helix | 284-287 | 4 | |
| β-strand | 296-314 | 19 | 6 |
| α-helix | 315-324 | 10 | |
| β-strand | 337-338 | 2 | 6 |
| α-helix | 339-347 | 9 | |
| β-strand | 362-366 | 5 | 9 |
| β-strand | 371-375 | 5 | 9 |
| β-strand | 389-398 | 10 | 6 |
| α-helix | 404-422 | 19 | |
| β-strand | 438-444 | 7 | 9 |
| β-strand | 449-455 | 7 | 9 |
| β-strand | 462-469 | 8 | 9 |
| β-strand | 475-480 | 6 | 9 |
| 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: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 932 | 1 | 50 |
18 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 27 | 0 | protein | 311 | Homo sapiens | Q6P2C8 (AlphaFold model) |
| Mediator of RNA polymerase II transcription subunit 28 | 1 | protein | 178 | Homo sapiens | Q9H204 (AlphaFold model) |
| Mediator of RNA polymerase II transcription subunit 29 | 2 | protein | 200 | Homo sapiens | Q9NX70 (AlphaFold model) |
| Mediator of RNA polymerase II transcription subunit 30 | 3 | protein | 178 | Homo sapiens | Q96HR3 (AlphaFold model) |
| Mediator of RNA polymerase II transcription subunit 31 | 4 | protein | 131 | Homo sapiens | Q9Y3C7 |
| Mediator of RNA polymerase II transcription subunit 1 | A | protein | 1581 | Homo sapiens | Q15648 |
| Unknown Chain | B | protein | 20 | Homo sapiens | |
| Mediator of RNA polymerase II transcription subunit 4 | D | protein | 270 | Homo sapiens | Q9NPJ6 |
| Mediator of RNA polymerase II transcription subunit 6 | F | protein | 246 | Homo sapiens | O75586 |
| Mediator of RNA polymerase II transcription subunit 7 | G | protein | 233 | Homo sapiens | O43513 |
| 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 |
14 more molecules are not listed.
Sequence of entity 1 (0), FASTA
>8TRH_1 Mediator of RNA polymerase II transcription subunit 27 (chains 0)
MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHFQDNL
HSVNRDLNELERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYH
AGLASGLLNQQSLKRSANQMGVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHL
SRPNGTSAMLLVTLGKVLKVIVVMRSLFIDRTIVKGYNENVYTEDGKLDIWSKSNYQVFQ
KVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAPCQRCGKFLQDGLPPTWRDFR
TLEAFHDTCRQ
Sequence of entity 2 (1), FASTA
>8TRH_2 Mediator of RNA polymerase II transcription subunit 28 (chains 1)
MAAPLGGMFSGQPPGPPQAPPGLPGQASLLQAAPGAPRPSSSTLVDELESSFEACFASLV
SQDYVNGTDQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQKPEQVIKEDVSELRN
ELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPADIPQGSLAYLEQASANIPAPLKPT
Sequence of entity 3 (2), FASTA
>8TRH_3 Mediator of RNA polymerase II transcription subunit 29 (chains 2)
MAASQQQASAASSAAGVSGPSSAGGPGPQQQPQPPAQLVGPAQSGLLQQQQQDFDPVQRY
KMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSDGPIQRFDKCLEEFYALCDQLELCL
RLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQYLAVIKAQISCAKDIHTALLD
CANKVTGKTPAPPAGPGGTL
Sequence of entity 4 (3), FASTA
>8TRH_4 Mediator of RNA polymerase II transcription subunit 30 (chains 3)
MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
DGSKNDDRAGPPRFASEERREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
Sequence of entity 5 (4), FASTA
>8TRH_5 Mediator of RNA polymerase II transcription subunit 31 (chains 4)
MAAAVAMETDDAGNRLRFQLELEFVQCLANPNYLNFLAQRGYFKDKAFVNYLKYLLYWKD
PEYAKYLKYPQCLHMLELLQYEHFRKELVNAQCAKFIDEQQILHWQHYSRKRMRLQQALA
EQQQQNNTSGK
Sequence of entity 6 (A), FASTA
>8TRH_6 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 7 (B), FASTA
>8TRH_7 Unknown Chain (chains B)
XXXXXXXXXXXXXXXXXXXX
Sequence of entity 8 (D), FASTA
>8TRH_8 Mediator of RNA polymerase II transcription subunit 4 (chains D)
MAASSSGEKEKERLGGGLGVAGGNSTRERLLSALEDLEVLSRELIEMLAISRNQKLLQAG
EENQVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQI
LATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDL
EMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDF
LLEPPGHNKENEDDVEIMSTDSSSSSSESD
Sequence of entity 9 (F), FASTA
>8TRH_9 Mediator of RNA polymerase II transcription subunit 6 (chains F)
MAAVDIRDNLLGISWVDSSWIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHL
NQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVL
TAVHGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDAL
LLDLRQKFPPKFVQLKPGEKPVPVDQTKKEAEPIPETVKPEEKETTKNVQQTVSAKGPPE
KRMRLQ
Sequence of entity 10 (G), FASTA
>8TRH_10 Mediator of RNA polymerase II transcription subunit 7 (chains G)
MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
SQGIERLHPMQFDHKKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
Sequence of entity 11 (H), FASTA
>8TRH_11 Mediator of RNA polymerase II transcription subunit 8 (chains H)
MQREEKQLEASLDALLSQVADLKNSLGSFICKLENEYGRLTWPSVLDSFALLSGQLNTLN
KVLKHEKTPLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQ
EKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTNA
LVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGVQ
MAQAGQPGKMPSGIKTNIKSASMHPYQR
Sequence of entity 12 (I), FASTA
>8TRH_12 Mediator of RNA polymerase II transcription subunit 9 (chains I)
MASAGVAAGRQAEDVLPPTSDQPLPDTKPLPPPQPPPVPAPQPQQSPAPRPQSPARAREE
ENYSFLPLVHNIIKCMDKDSPEVHQDLNALKSKFQEMRKLISTMPGIHLSPEQQQQQLQS
LREQVRTKNELLQKYKSLCMFEIPKE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module. Chao, T.C., Chen, S.F., Kim, H.J. et al. Mol Cell (2024) 84:3932-3949.e10. DOI 10.1016/j.molcel.2024.09.001 · PubMed
Other PDB entries of the same protein (UniProt Q6P2C8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7EMF 3.5 Å, Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation
- 7ENA 4.07 Å, TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)
- 7ENC 4.13 Å, TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
- 8GXS 4.16 Å, PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state
- 7ENJ 4.4 Å, Human Mediator (deletion of MED1-IDR) in a Tail-bent conformation (MED-B)
- 7NVR 4.5 Å, Human Mediator with RNA Polymerase II Pre-initiation complex
- 8T9D 4.66 Å, CryoEM structure of TR-TRAP
- 7LBM 4.8 Å, Structure of the human Mediator-bound transcription pre-initiation complex
- 8GXQ 5.04 Å, PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
- 8TQW 8.2 Å, Structure of human transcriptional Mediator complex
Browse structure collections
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