6XI8: Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex

Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex. Determined by electron microscopy at 3.64 Å resolution. Released 28 Apr 2021.

Method: Electron microscopy
Resolution: 3.64 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 3
Atoms: 5,022
Mol. weight: 79.98 kDa
Ligands: AF3, ADP
Released: 28 Apr 2021

Explore 6XI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XI8 contains 36 α-helices and 13 β-strands across 3 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: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	1
β-strand	19-21	3	1
β-strand	24	1	2
β-strand	33	1	2
β-strand	36-38	3	1
α-helix	49-55	7
β-strand	66	1	3
β-strand	74	1	1
β-strand	79-80	2	1
β-strand	88	1	3
α-helix	89-94	6
α-helix	105-122	18
β-strand	125	1	4
β-strand	135-136	2	3
β-strand	144-145	2	3
β-strand	153	1	4
α-helix	168-170	3
α-helix	173-177	5
α-helix	186-200	15
α-helix	212-220	9
α-helix	223-225	3
α-helix	245-247	3
α-helix	249-251	3
α-helix	263-270	8
α-helix	279-280	2
α-helix	281-283	3
α-helix	295-296	2

Chain B: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	53-56	4
α-helix	62-72	11
α-helix	78-83	6
α-helix	95-105	11
α-helix	109-130	22
α-helix	135-151	17
α-helix	159-173	15
α-helix	180-185	6
α-helix	199-205	7
α-helix	215-221	7
α-helix	224-228	5
α-helix	236-239	4
α-helix	245-254	10
α-helix	263-270	8
α-helix	271-273	3
α-helix	279-286	8
α-helix	329-344	16
α-helix	353-359	7
α-helix	365-369	5

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	285-287	3
α-helix	289-292	4
α-helix	298-308	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase II transcription factor B subunit 3	C	protein	63	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q03290 (AlphaFold model)
Serine/threonine-protein kinase KIN28	A	protein	301	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P06242 (AlphaFold model)
Cyclin CCL1	B	protein	324	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P37366 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6XI8_1 RNA polymerase II transcription factor B subunit 3 (chains C)
PFNGDREAHPPFTLKGSVYNDPFIKDLEHRKEFIASGFNTNYAYERVLTEAFMGLGCVIS
EEL

Sequence of entity 2 (A), FASTA

>6XI8_2 Serine/threonine-protein kinase KIN28 (chains A)
VNMEYTKEKKVGEGTYAVVYLGCQHSTGRKIAIKEIKTSEFKDGLDMSAIREVKYLQEMQ
HPNVIELIDIFMAYDNLNLVLEFLPTDLEVVIKDKSILFTPADIKAWMLMTLRGVYHCHR
NFILHRDLKPNNLLFSPDGQIKVADFGLARAIPAPHEILTSNVVTRWYRAPELLFGAKHY
TSAIDIWSVGVIFAELMLRIPYLPGQNDVDQMEVTFRALGTPTDRDWPEVSSFMTYNKLQ
IYPPPSRDELRKRFIAASEYALDFMCGMLTMNPQKRWTAVQCLESDYFKELPPPSDPSSI
K

Sequence of entity 3 (B), FASTA

>6XI8_3 Cyclin CCL1 (chains B)
DLYRHSSQYRMWSYTKDQLQEKRVDTNARAIAYIEENLLKFREAHNLTEEEIKVLEAKAI
PLTMEEELDLVNFYAKKVQVIAQHLNLPTEVVATAISFFRRFFLENSVMQIDPKSIVHTT
IFLACKSENYFISVDSFAQKAKSTRDSVLKFEFKLLESLKFSLLNHHPYKPLHGFFLDIQ
NVLYGKVDLNYMGQIYDRCKKRITAALLTDVVYFYTPPQITLATLLIEDEALVTRYLETK
FPSREGSQESVPGNEKEEPQNDASTTEKNKEKSTESEEYSIDSAKLLTIIRECKSIIEDC
KPPSTEEAKKIAAKNYYCQNPSTL

Ligands and cofactors

ID	Name	Formula	Copies
AF3	Aluminum fluoride	Al F3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Structure of TFIIK for phosphorylation of CTD of RNA polymerase II. van Eeuwen, T., Li, T., Kim, H.J. et al. Sci Adv (2021) 7. DOI 10.1126/sciadv.abd4420 · PubMed

Other PDB entries of the same protein (UniProt Q03290 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O4J 2.9 Å, Yeast RNA polymerase II transcription pre-initiation complex (consensus)
7ML0 3.0 Å, RNA polymerase II pre-initiation complex (PIC1)
8CEN 3.0 Å, Yeast RNA polymerase II transcription pre-initiation complex with core Mediator
7ML4 3.1 Å, RNA polymerase II initially transcribing complex (ITC)
7ZS9 3.1 Å, Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome…
7O4I 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with initial transcription…
7O75 3.2 Å, Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA
7ML2 3.4 Å, RNA polymerase II pre-initiation complex (PIC3)
7O4L 3.4 Å, Yeast TFIIH in the expanded state within the pre-initiation complex
7O72 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA
7O73 3.4 Å, Yeast RNA polymerase II transcription pre-initiation complex with closed distorted…
7KUE 3.5 Å, CryoEM structure of Yeast TFIIK (Kin28/Ccl1/Tfb3) Complex

Browse structure collections

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