3J1O: PDB entry 3J1O

Cryo-EM map of a yeast minimal preinitiation complex interacting with the Mediator Head module. Determined by electron microscopy at 16.0 Å resolution. Released 6 Mar 2013.

Method: Electron microscopy
Resolution: 16.0 Å
Organism: Saccharomyces cerevisiae
Chains: 7
Atoms: 5,560
Mol. weight: 165.69 kDa
Released: 6 Mar 2013

Explore 3J1O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J1O contains 53 α-helices and 36 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 H: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	22-25	4
α-helix	37-40	4
α-helix	45-52	8
α-helix	61-72	12
α-helix	73-75	3
α-helix	113-115	3
α-helix	119-128	10

Chain I: 17 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	200-207	8
α-helix	216-228	13
α-helix	272-275	4
α-helix	287-299	13
α-helix	302-311	10
α-helix	312-314	3
β-strand	424	1	1
α-helix	425-428	4
α-helix	435-453	19
α-helix	469	1
α-helix	472	1
α-helix	485-487	3
α-helix	503-524	22
α-helix	556-563	8
α-helix	566-569	4
α-helix	571-574	4
α-helix	601-611	11
β-strand	1621-1622	2	2
β-strand	1721-1722	2	2
α-helix	675-683	9

Chain J: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	38-54	17
α-helix	63-82	20
α-helix	107-109	3
α-helix	112-116	5
α-helix	121-123	3
α-helix	147-158	12
α-helix	164-167	4
α-helix	196-198	3
α-helix	199-203	5

Chain K: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-11	6
α-helix	15-21	7
α-helix	49-77	29
α-helix	105-108	4

Chain L: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	10-11	2	4
α-helix	16-25	10
β-strand	33	1	3
β-strand	36	1	5
β-strand	39-41	3	6
α-helix	42	1
α-helix	44	1
α-helix	62-63	2
β-strand	64-66	3	6
α-helix	72-75	4
α-helix	79-82	4
β-strand	166-170	5	3
β-strand	182-188	7	3
β-strand	193-195	3	7
α-helix	202-205	4
β-strand	214	1	6
β-strand	216-217	2	5
β-strand	220-224	5	3
β-strand	228-232	5	3
β-strand	233	1	4
β-strand	235-237	3	5
β-strand	244-245	2	5
β-strand	251-252	2	4
β-strand	255-258	4	3
α-helix	259	1
α-helix	273-282	10
β-strand	284-285	2	1
α-helix	290-292	3

Chain M: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
α-helix	21-24	4
β-strand	37-43	7	7
β-strand	57-62	6	7
β-strand	69-73	5	7
β-strand	76-79	4	7
α-helix	90-93	4
β-strand	101	1	3
α-helix	104-111	8
β-strand	117-122	6	7
β-strand	123	1	9
β-strand	128-130	3	8
β-strand	135-140	6	8
β-strand	143	1	9
β-strand	148	1	9
β-strand	151-157	7	8
α-helix	163-166	4
β-strand	184	1	8
α-helix	202-205	4

Chain N: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	176-186	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mediator of RNA polymerase II transcription subunit 11	H	protein	131	Saccharomyces cerevisiae	Q99278 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 17	I	protein	484	Saccharomyces cerevisiae	P32569 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 8	J	protein	223	Saccharomyces cerevisiae	P38304 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 22	K	protein	121	Saccharomyces cerevisiae	P32570 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 18	L	protein	275	Saccharomyces cerevisiae	P32585
Mediator of RNA polymerase II transcription subunit 20	M	protein	210	Saccharomyces cerevisiae	P34162
Mediator of RNA polymerase II transcription subunit 6	N	protein	25	Saccharomyces cerevisiae	P38782

Sequence of entity 1 (H), FASTA

>3J1O_1 Mediator of RNA polymerase II transcription subunit 11 (chains H)
MQVLNTKSETKQENEGSQPPYIQERLKSLNDIETQLCSMLQEASQVTFIFGELKRGNESV
KPQFENHVKQFYERLDKSTTQLRKEIQLLDENVGTRLLPINVNKKALGQDTEKMEEQLDL
LSAILDPSKSK

Sequence of entity 2 (I), FASTA

>3J1O_2 Mediator of RNA polymerase II transcription subunit 17 (chains I)
QEQFVKRRRDMLEHINLAMNESSLALEFVSLLLSSVKESTGMSSMSPFLRKVVKPSSLNS
DKIPYVAPTKKEYIELDILNKGWKLQSLNESKDLLRASFNKLSSILQNEHDYWNKIMQSI
SNKDVIFKIRDRTSGQKLLAIKYGYEDSGSTYKHDRGIANIRNNIESQNLDLIPHSSSVF
KGTDFVHSVKKFLRVRIFTKIESEDDYILSGESVMDRDSESEEAETKDIRKQIQLLKKII
FEKELMYQIKKECALLISYGVSIENENKVIIELPNEKFEIELLSLDDDSIVNHEQDLPKI
NDKRANLMLVMLRLLLVVIFKKTLRSRISSPHGLINLNVDDDILIIRPILGKVRFANYKL
LLKKIIKDYVLDIVPGSSITETEVEREQPQENKNIDDENITKLNKEIRAFDKLLNIPRRE
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEVEDFLHFIVAEYIQ
QKKV

Sequence of entity 3 (J), FASTA

>3J1O_3 Mediator of RNA polymerase II transcription subunit 8 (chains J)
MSQSTASLVPEGNQGSLQEDVSFDFNGVPGQALDAVRMRLAQLTHSLRRIRDEMSKAELP
QWYTLQSQLNVTLSQLVSVTSTLQHFQETLDSTVVYPLPKFPTTSHESLVTTLLRKKNIP
EVDEWMKYVRETSGVTTALLKDEEIEKLLQQDREITNWARTTFRNEYGKHDFKNEESLSE
EHASLLVRDSKPSKPFNVDDVLKFTFTGEKPIITGSTSTSSSN

Sequence of entity 4 (K), FASTA

>3J1O_4 Mediator of RNA polymerase II transcription subunit 22 (chains K)
MSNQALYEKLEQTRTILSVKLAELINMTTIADRNDDDEGSFAQENSELAVATTSVMMVNN
QTMQLIKNVQDLLILTRSIKEKWLLNQIPVTEHSKVTRFDEKQIEELLDNCIETFVAEKT
T

Sequence of entity 5 (L), FASTA

>3J1O_5 Mediator of RNA polymerase II transcription subunit 18 (chains L)
MVQQLSLFGSIGDDGYDLLISTLTTISGNPPLLYNSLCTVWKPNPSYDVENVNSRNQLVE
PNRIKLSKEVPFSYLIDETMMDKPLNFRILKSFTNDKIPLNYAMTRNINSDDIIDVDMDA
SPAPSNESCSPWSLQISDIPAAGNNRSVSMQTIAETIILSSAGKNSSVSSLMNGLGYVFE
FQYLTIGVKFFMKHGLILELQKIWQIEEAGNSQITSGGFLLKAYINVSRGTDIDRINYTE
TALMNLKKELQGYIELSVPDRQSMDSRVAHGNILI

Sequence of entity 6 (M), FASTA

>3J1O_6 Mediator of RNA polymerase II transcription subunit 20 (chains M)
MGKSAVIFVERATPATLTELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSI
TFHHHGRQTVLIKDNSAMVTTAAAADIPPALVFNGSSTGVPESIDTILSSKLSNIWMQRQ
LIKGDAGETLILDGLTVRLVNLFSSTGFKGLLIELQADEAGEFETKIAGIEGHLAEIRAK
EYKTSSDSLGPDTSNEICDLAYQYVRALEL

Sequence of entity 7 (N), FASTA

>3J1O_7 Mediator of RNA polymerase II transcription subunit 6 (chains N)
IFKIVQSRLMSTSYHLNSTLESLYD

Primary citation

Interaction of the mediator head module with RNA polymerase II. Cai, G., Chaban, Y.L., Imasaki, T. et al. Structure (2012) 20:899-910. DOI 10.1016/j.str.2012.02.023 · 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)
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)

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