4GWP: Mediator Head Module from S. cerevisiae

Structure of the Mediator Head Module from S. cerevisiae. Determined by X-ray diffraction at 4.2 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 4.2 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae S288c
Chains: 7
Atoms: 9,033
Mol. weight: 241.79 kDa
Released: 31 Oct 2012

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

Secondary structure: helices and β-sheets

4GWP contains 56 α-helices and 45 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: 16 helices, 17 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	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	542-546	5
α-helix	547-549	3
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	123-130	8
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	57-64	8	7
β-strand	66-73	8	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, 7 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	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	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

Sequence of entity 1 (A), FASTA

>4GWP_1 Mediator of RNA polymerase II transcription subunit 11 (chains A)
MQPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESVKPQFENHVKQFYERLD
KSTTQLRKEIQLLDENVGTRLLPINVNKKALGQDTEKMEEQLDLLSAILDPSKSK

Sequence of entity 2 (B), FASTA

>4GWP_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

>4GWP_3 Mediator of RNA polymerase II transcription subunit 8 (chains C)
MSQSTASLVPEGNQGSLQEDVSFDFNGVPGQALDAVRMRLAQLTHSLRRIRDEMSKAELP
QWYTLQSQLNVTLSQLVSVTSTLQHFQETLDSTVVYPLPKFPTTSHESLVTTLLRKKNIP
EVDEWMKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDFKNEESLSE
EHASLLVRDSKPSKPFNVDDVLKFTFTGEKPIITGSTSTSSSNSMEKRRWKKNFIAVSAA
NRFKKISSSGALDYDIPTTASENLYFQGELKTAALAQHDEAVDNKFNKEQQNAFYEILHL
PNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDNKFNKEQQNAFYEILHLPN
LNEEQRNAFIQSLKDDPSQSANLLAEAKKLNGAQAPKVDANSAGKST

Sequence of entity 4 (D), FASTA

>4GWP_4 Mediator of RNA polymerase II transcription subunit 22 (chains D)
MSNQALYEKLEQTRTILSVKLAELINMTTIADRNDDDEGSFAQENSELAVATTSVMMVNN
QTMQLIKNVQDLLILTRSIKEKWLLNQIPVTEHSKVTRFDEKQIEELLDNCIETFVAEKT
T

Sequence of entity 5 (E), FASTA

>4GWP_5 Mediator of RNA polymerase II transcription subunit 18 (chains E)
MVQQLSLFGSIGDDGYDLLISTLTTISGNPPLLYNSLCTVWKPNPSYDVENVNSRNQLVE
PNRIKLSKEVPFSYLIDETMMDKPLNFRILKSFTNDKIPLNYAMTRNILHNTVPQVTNFN
STNEDQNNSKHTEDTVNESRNSDDIIDVDMDASPAPSNESCSPWSLQISDIPAAGNNRSV
SMQTIAETIILSSAGKNSSVSSLMNGLGYVFEFQYLTIGVKFFMKHGLILELQKIWQIEE
AGNSQITSGGFLLKAYINVSRGTDIDRINYTETALMNLKKELQGYIELSVPDRQSMDSRV
AHGNILI

Sequence of entity 6 (F), FASTA

>4GWP_6 Mediator of RNA polymerase II transcription subunit 20 (chains F)
MGKSAVIFVERATPATLTELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSI
TFHHHGRQTVLIKDNSAMVTTAAAADIPPALVFNGSSTGVPESIDTILSSKLSNIWMQRQ
LIKGDAGETLILDGLTVRLVNLFSSTGFKGLLIELQADEAGEFETKIAGIEGHLAEIRAK
EYKTSSDSLGPDTSNEICDLAYQYVRALEL

Sequence of entity 7 (G), FASTA

>4GWP_7 Mediator of RNA polymerase II transcription subunit 6 (chains G)
MNVTPLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNA
AVNMTQNIMTLPDGKNGNLEEEFAYVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSV
REPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSPTIFKIVQSRLMSTSYH
LNSTLESLYDLIEFQPSQGVHYKVPTDTSTTATAATNGNNAGGGSNKSSVRPTGGANMAT
VPSTTNVNMTVNTMGTGGQTIDNGTGRTGNGNMGITTEMLDKLMVTSIRSTPNYI

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…
3RJ1 4.3 Å, Architecture of the Mediator Head module
7UIG 4.3 Å, Mediator-PIC Early (Mediator A)
4GWQ 4.5 Å, Structure of the Mediator Head Module from S. cerevisiae in complex with the…
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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