8TQW: Human transcriptional Mediator complex

Name: PDB 8TQW: Structure of human transcriptional Mediator complex
Published: 2024-10-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Structure of human transcriptional Mediator complex. Determined by electron microscopy at 8.2 Å resolution. Released 9 Oct 2024.

Method: Electron microscopy
Resolution: 8.2 Å
Organism: Homo sapiens
Chains: 29
Atoms: 83,816
Mol. weight: 1808.05 kDa
Ligands: ZN
Released: 9 Oct 2024

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

Secondary structure: helices and β-sheets

8TQW contains 497 α-helices and 241 β-strands across 29 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: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-36	28
β-strand	40	1	1
α-helix	46-76	31
α-helix	112-123	12
α-helix	159-169	11
β-strand	176	1	2
β-strand	179-181	3	2
β-strand	189-194	6	2
β-strand	198-205	8	2
β-strand	208-215	8	2
β-strand	222	1	3
β-strand	228	1	3
α-helix	229	1
α-helix	237-250	14
α-helix	259-271	13
α-helix	272-275	4
β-strand	289	1	4
β-strand	292	1	4
β-strand	296-298	3	5
β-strand	301-305	5	5

Chain 1: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	44-57	14
α-helix	71-105	35
α-helix	108-136	29
α-helix	138-143	6

Chain 2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	56-89	34
α-helix	102-129	28
α-helix	157-185	29

Chain 3: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	30-55	26
α-helix	70-100	31
α-helix	138-175	38

Chain 4: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	11-28	18
α-helix	31-40	10
α-helix	46-54	9
α-helix	56-58	3
α-helix	61-64	4
α-helix	71-80	10
α-helix	83-86	4
α-helix	91-105	15
α-helix	107-121	15

Chain a: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	20	1	70
β-strand	26-29	4	71
β-strand	33-38	6	71
β-strand	40	1	70
β-strand	49-54	6	71
α-helix	61-69	9
β-strand	78	1	72
β-strand	81-87	7	71
β-strand	92-98	7	71
β-strand	102-103	2	72
α-helix	104-110	7
α-helix	125-144	20
β-strand	147-148	2	73
α-helix	154-156	3
β-strand	157-160	4	72
β-strand	167-171	5	72
β-strand	178-179	2	73
α-helix	202-205	4
α-helix	215-229	15
α-helix	252-259	8
α-helix	277-279	3
α-helix	292-298	7
α-helix	307-315	9
α-helix	326-329	4
α-helix	349-351	3
α-helix	354-358	5

Chain A: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	14-26	13
α-helix	34-45	12
α-helix	57-65	9
α-helix	67-69	3
α-helix	71-72	2
α-helix	74-88	15
β-strand	91	1	17
β-strand	94	1	17
β-strand	100-103	4	17
β-strand	108-111	4	17
α-helix	136-143	8
α-helix	147-160	14
α-helix	169-194	26
α-helix	199-203	5
β-strand	212	1	18
α-helix	213-214	2
β-strand	215	1	19
β-strand	218	1	19
α-helix	219	1
β-strand	220-223	4	18
α-helix	228-231	4
β-strand	254-269	16	18
α-helix	285-287	3
β-strand	296-314	19	18
α-helix	315-325	11
β-strand	337-338	2	18
α-helix	339-346	8
β-strand	362-366	5	20
β-strand	371-375	5	20
β-strand	389-398	10	18
α-helix	404-424	21
β-strand	438-444	7	20
β-strand	449-455	7	20
β-strand	462-468	7	20
β-strand	477	1	20
β-strand	480-481	2	20
α-helix	491-500	10
α-helix	505-517	13

Chain b: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	9	1
α-helix	10-14	5
α-helix	18-24	7
α-helix	34-54	21
α-helix	59-74	16
α-helix	83-97	15
α-helix	102-104	3
α-helix	105-115	11
α-helix	132-144	13
α-helix	156-166	11
α-helix	173-183	11
α-helix	188-190	3
α-helix	194-208	15
α-helix	214-219	6
α-helix	225-242	18
α-helix	246-253	8
α-helix	259-261	3

21 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

17 more molecules are not listed.

Sequence of entity 1 (0), FASTA

>8TQW_1 Mediator of RNA polymerase II transcription subunit 27 (chains 0)
MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHFQDNL
HSVNRDLNELERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYH
AGLASGLLNQQSLKRSANQMGVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHL
SRPNGTSAMLLVTLGKVLKVIVVMRSLFIDRTIVKGYNENVYTEDGKLDIWSKSNYQVFQ
KVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAPCQRCGKFLQDGLPPTWRDFR
TLEAFHDTCRQ

Sequence of entity 2 (1), FASTA

>8TQW_2 Mediator of RNA polymerase II transcription subunit 28 (chains 1)
MAAPLGGMFSGQPPGPPQAPPGLPGQASLLQAAPGAPRPSSSTLVDELESSFEACFASLV
SQDYVNGTDQEEIRTGVDQCIQKFLDIARQTECFFLQKRLQLSVQKPEQVIKEDVSELRN
ELQRKDALVQKHLTKLRHWQQVLEDINVQHKKPADIPQGSLAYLEQASANIPAPLKPT

Sequence of entity 3 (2), FASTA

>8TQW_3 Mediator of RNA polymerase II transcription subunit 29 (chains 2)
MAASQQQASAASSAAGVSGPSSAGGPGPQQQPQPPAQLVGPAQSGLLQQQQQDFDPVQRY
KMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSDGPIQRFDKCLEEFYALCDQLELCL
RLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQYLAVIKAQISCAKDIHTALLD
CANKVTGKTPAPPAGPGGTL

Sequence of entity 4 (3), FASTA

>8TQW_4 Mediator of RNA polymerase II transcription subunit 30 (chains 3)
MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
DGSKNDDRAGPPRFASEERREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN

Sequence of entity 5 (4), FASTA

>8TQW_5 Mediator of RNA polymerase II transcription subunit 31 (chains 4)
MAAAVAMETDDAGNRLRFQLELEFVQCLANPNYLNFLAQRGYFKDKAFVNYLKYLLYWKD
PEYAKYLKYPQCLHMLELLQYEHFRKELVNAQCAKFIDEQQILHWQHYSRKRMRLQQALA
EQQQQNNTSGK

Sequence of entity 6 (A), FASTA

>8TQW_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

>8TQW_7 Unknown Chain (chains B)
XXXXXXXXXXXXXXXXXXXX

Sequence of entity 8 (D), FASTA

>8TQW_8 Mediator of RNA polymerase II transcription subunit 4 (chains D)
MAASSSGEKEKERLGGGLGVAGGNSTRERLLSALEDLEVLSRELIEMLAISRNQKLLQAG
EENQVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQI
LATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDL
EMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDF
LLEPPGHNKENEDDVEIMSTDSSSSSSESD

Sequence of entity 9 (F), FASTA

>8TQW_9 Mediator of RNA polymerase II transcription subunit 6 (chains F)
MAAVDIRDNLLGISWVDSSWIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHL
NQMVGIEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVINSRVL
TAVHGIQSAFDEAMSYCRYHPSKGYWWHFKDHEEQDKVRPKAKRKEEPSSIFQRQRVDAL
LLDLRQKFPPKFVQLKPGEKPVPVDQTKKEAEPIPETVKPEEKETTKNVQQTVSAKGPPE
KRMRLQ

Sequence of entity 10 (G), FASTA

>8TQW_10 Mediator of RNA polymerase II transcription subunit 7 (chains G)
MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
SQGIERLHPMQFDHKKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP

Sequence of entity 11 (H), FASTA

>8TQW_11 Mediator of RNA polymerase II transcription subunit 8 (chains H)
MQREEKQLEASLDALLSQVADLKNSLGSFICKLENEYGRLTWPSVLDSFALLSGQLNTLN
KVLKHEKTPLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQ
EKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTNA
LVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGVQ
MAQAGQPGKMPSGIKTNIKSASMHPYQR

Sequence of entity 12 (I), FASTA

>8TQW_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	4

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
8TRH 3.7 Å, The IDRc bound human core Mediator complex
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

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