4GWQ: Mediator Head Module from S. cerevisiae

Structure of the Mediator Head Module from S. cerevisiae in complex with the carboxy-terminal domain (CTD) of RNA Polymerase II Rpb1 subunit. Determined by X-ray diffraction at 4.5 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 4.5 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae S288c
Chains: 8
Atoms: 9,217
Mol. weight: 245.41 kDa
Released: 31 Oct 2012

Explore 4GWQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GWQ contains 55 α-helices and 48 β-strands across 7 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-37	31
α-helix	42-44	3
α-helix	45-78	34
α-helix	83-84	2
α-helix	93-112	20

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	183-189	7
α-helix	199-228	30
α-helix	232-238	7
α-helix	242-245	4
α-helix	258-266	9
α-helix	268-313	46
β-strand	324-327	4	1
β-strand	335-338	4	1
β-strand	355-358	4	2
β-strand	364-367	4	2
β-strand	379	1	2
β-strand	387-388	2	3
β-strand	393-396	4	4
β-strand	405-408	4	4
α-helix	425-451	27
β-strand	459	1	5
β-strand	463	1	5
β-strand	465-468	4	4
β-strand	473-477	5	4
β-strand	484-485	2	3
α-helix	496-525	30
α-helix	535-537	3
α-helix	542-549	8
α-helix	550-554	5
α-helix	555-567	13
β-strand	575-577	3	6
α-helix	580-583	4
α-helix	597-614	18
β-strand	620-623	4	6
β-strand	629-636	8	6
β-strand	643-650	8	6
β-strand	656-660	5	6
α-helix	671-684	14

Chain C: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	33-55	23
α-helix	60-62	3
α-helix	63-86	24
α-helix	88-94	7
α-helix	102-104	3
α-helix	110-114	5
α-helix	123-132	10
α-helix	141-167	27
α-helix	183-190	8
α-helix	198-207	10

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-30	29
α-helix	47-84	38
α-helix	89-91	3
α-helix	104-116	13

Chain E: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	7
α-helix	13-27	15
β-strand	32-43	12	7
β-strand	62	1	8
β-strand	64-68	5	7
α-helix	72-74	3
α-helix	86-93	8
α-helix	103-106	4
β-strand	164-169	6	7
α-helix	171-174	4
β-strand	181-195	15	7
α-helix	200-206	7
β-strand	209-223	15	7
α-helix	225-227	3
β-strand	229-238	10	7
β-strand	243-245	3	7
β-strand	250-259	10	7
α-helix	265-281	17
β-strand	289	1	7
α-helix	290-292	3
α-helix	293-296	4
β-strand	299	1	8

Chain F: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	16-22	7
β-strand	30-44	15	7
β-strand	57-62	6	7
β-strand	68-73	6	7
β-strand	76-81	6	7
α-helix	84-86	3
α-helix	89-93	5
α-helix	104-111	8
β-strand	116-132	17	7
β-strand	135-145	11	7
β-strand	147-157	11	7
α-helix	163-176	14
β-strand	183-185	3	7
α-helix	196-207	12

Chain G: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	9
α-helix	24-33	10
α-helix	39-49	11
α-helix	89-94	6
α-helix	100-110	11
β-strand	113-115	3	10
β-strand	118-120	3	10
β-strand	124-130	7	9
β-strand	133-141	9	9
β-strand	144	1	11
β-strand	147	1	11
β-strand	150-158	9	9
β-strand	161-163	3	9
α-helix	169-188	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mediator of RNA polymerase II transcription subunit 11	A	protein	115	Saccharomyces cerevisiae	Q99278 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 17	B	protein	687	Saccharomyces cerevisiae S288c	P32569 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 8	C	protein	407	Saccharomyces cerevisiae	P38304 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 22	D	protein	121	Saccharomyces cerevisiae	P32570 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 18	E	protein	307	Saccharomyces cerevisiae	P32585
Mediator of RNA polymerase II transcription subunit 20	F	protein	210	Saccharomyces cerevisiae	P34162
Mediator of RNA polymerase II transcription subunit 6	G	protein	295	Saccharomyces cerevisiae S288c	P38782
DNA-directed RNA polymerase II subunit RPB1	H	protein	35	Saccharomyces cerevisiae	P04050

Sequence of entity 1 (A), FASTA

>4GWQ_1 Mediator of RNA polymerase II transcription subunit 11 (chains A)
MQPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLD
KSTTQLRKEIQLLDENVGTRLLPINVNKKALGQDTEKMEEQLDLLSAILDPSKSK

Sequence of entity 2 (B), FASTA

>4GWQ_2 Mediator of RNA polymerase II transcription subunit 17 (chains B)
MTTEDPDSNHLSSETGIKLALDPNLITLALSSNPNSSLHSPTSDEPVPESAGKADTSIRL
EGDELENKTKKDNDKNLKFLKNKDSLVSNPHEIYGSMPLEQLIPIILRQRGPGFKFVDLN
EKELQNEIKQLGSDSSDGHNSEKKDTDGADENVQIGEDFMEVDYEDKDNPVDSRNETDHK
TNENGETDDNIETVMTQEQFVKRRRDMLEHINLAMNESSLALEFVSLLLSSVKESTGMSS
MSPFLRKVVKPSSLNSDKIPYVAPTKKEYIELDILNKGWKLQSLNESKDLLRASFNKLSS
ILQNEHDYWNKIMQSISNKDVIFKIRDRTSGQKLLAIKYGYEDSGSTYKHDRGIANIRNN
IESQNLDLIPHSSSVFKGTDFVHSVKKFLRVRIFTKIESEDDYILSGESVMDRDSESEEA
ETKDIRKQIQLLKKIIFEKELMYQIKKECALLISYGVSIENENKVIIELPNEKFEIELLS
LDDDSIVNHEQDLPKINDKRANLMLVMLRLLLVVIFKKTLRSRISSPHGLINLNVDDDIL
IIRPILGKVRFANYKLLLKKIIKDYVLDIVPGSSITETEVEREQPQENKNIDDENITKLN
KEIRAFDKLLNIPRRELKINLPLTEHKSPNLSLMLESPNYCNALIHIKFSAGTEANAVSF
DTTFSDFKEVEDFLHFIVAEYIQQKKV

Sequence of entity 3 (C), FASTA

>4GWQ_3 Mediator of RNA polymerase II transcription subunit 8 (chains C)
MSQSTASLVPEGNQGSLQEDVSFDFNGVPGQALDAVRMRLAQLTHSLRRIRDEMSKAELP
QWYTLQSQLNVTLSQLVSVTSTLQHFQETLDSTVVYPLPKFPTTSHESLVTTLLRKKNIP
EVDEWMKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDFKNEESLSE
EHASLLVRDSKPSKPFNVDDVLKFTFTGEKPIITGSTSTSSSNSMEKRRWKKNFIAVSAA
NRFKKISSSGALDYDIPTTASENLYFQGELKTAALAQHDEAVDNKFNKEQQNAFYEILHL
PNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDNKFNKEQQNAFYEILHLPN
LNEEQRNAFIQSLKDDPSQSANLLAEAKKLNGAQAPKVDANSAGKST

Sequence of entity 4 (D), FASTA

>4GWQ_4 Mediator of RNA polymerase II transcription subunit 22 (chains D)
MSNQALYEKLEQTRTILSVKLAELINMTTIADRNDDDEGSFAQENSELAVATTSVMMVNN
QTMQLIKNVQDLLILTRSIKEKWLLNQIPVTEHSKVTRFDEKQIEELLDNCIETFVAEKT
T

Sequence of entity 5 (E), FASTA

>4GWQ_5 Mediator of RNA polymerase II transcription subunit 18 (chains E)
MVQQLSLFGSIGDDGYDLLISTLTTISGNPPLLYNSLCTVWKPNPSYDVENVNSRNQLVE
PNRIKLSKEVPFSYLIDETMMDKPLNFRILKSFTNDKIPLNYAMTRNILHNTVPQVTNFN
STNEDQNNSKHTEDTVNESRNSDDIIDVDMDASPAPSNESCSPWSLQISDIPAAGNNRSV
SMQTIAETIILSSAGKNSSVSSLMNGLGYVFEFQYLTIGVKFFMKHGLILELQKIWQIEE
AGNSQITSGGFLLKAYINVSRGTDIDRINYTETALMNLKKELQGYIELSVPDRQSMDSRV
AHGNILI

Sequence of entity 6 (F), FASTA

>4GWQ_6 Mediator of RNA polymerase II transcription subunit 20 (chains F)
MGKSAVIFVERATPATLTELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSI
TFHHHGRQTVLIKDNSAMVTTAAAADIPPALVFNGSSTGVPESIDTILSSKLSNIWMQRQ
LIKGDAGETLILDGLTVRLVNLFSSTGFKGLLIELQADEAGEFETKIAGIEGHLAEIRAK
EYKTSSDSLGPDTSNEICDLAYQYVRALEL

Sequence of entity 7 (G), FASTA

>4GWQ_7 Mediator of RNA polymerase II transcription subunit 6 (chains G)
MNVTPLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNA
AVNMTQNIMTLPDGKNGNLEEEFAYVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSV
REPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLMSTSYH
LNSTLESLYDLIEFQPSQGVHYKVPTDTSTTATAATNGNNAGGGSNKSSVRPTGGANMAT
VPSTTNVNMTVNTMGTGGQTIDNGTGRTGNGNMGITTEMLDKLMVTSIRSTPNYI

Sequence of entity 8 (H), FASTA

>4GWQ_8 DNA-directed RNA polymerase II subunit RPB1 (chains H)
YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

Primary citation

Structure of the Mediator Head module bound to the carboxy-terminal domain of RNA polymerase II. Robinson, P.J., Bushnell, D.A., Trnka, M.J. et al. Proc Natl Acad Sci U S A (2012) 109:17931-17935. DOI 10.1073/pnas.1215241109 · PubMed

Other PDB entries of the same protein (UniProt Q99278 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3R84 2.05 Å, Structure of the Mediator head subcomplex Med11/22
4H62 3.0 Å, Structure of the Saccharomyces cerevisiae Mediator subcomplex Med17C/Med11C/Med22C
8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
7UI9 3.3 Å, Core Mediator-PICearly (Copy A)
7UIO 3.3 Å, Mediator-PIC Early (Composite Model)
9PC8 3.4 Å, Core Mediator of PIC-Med-SWI/SNF
8CEO 3.6 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the…
4GWP 4.2 Å, Structure of the Mediator Head Module from S. cerevisiae
3RJ1 4.3 Å, Architecture of the Mediator Head module
7UIG 4.3 Å, Mediator-PIC Early (Mediator A)
7UIF 4.6 Å, Mediator-PIC Early (Core B)
5OQM 5.8 Å, Structure of yeast transcription pre-initiation complex with tfiih and core mediator

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