1Y14: Yeast subcomplex of Rpb4 and Rpb7

Crystal structure of yeast subcomplex of Rpb4 and Rpb7. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Dec 2004.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 4,776
Mol. weight: 81.04 kDa
Released: 14 Dec 2004

Explore 1Y14 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y14 contains 23 α-helices and 30 β-strands across 4 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: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	47-50	4	1
α-helix	52-71	20
α-helix	119-133	15
α-helix	139-151	13
α-helix	157-168	12
α-helix	174-182	9
α-helix	188-194	7
α-helix	196-198	3
α-helix	204-217	14

Chain B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	1
α-helix	22-34	13
β-strand	37-39	3	1
β-strand	43-48	6	1
α-helix	51-53	3
β-strand	55	1	1
β-strand	71-79	9	1
β-strand	86-95	10	2
β-strand	98-103	6	2
β-strand	106-111	6	2
α-helix	112-114	3
β-strand	120-121	2	3
β-strand	130-131	2	3
β-strand	136-137	2	3
β-strand	142-153	12	2
β-strand	156-162	7	2
β-strand	169-170	2	2

Chain C: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	48-50	3	4
α-helix	52-73	22
α-helix	75-76	2
α-helix	120-133	14
α-helix	139-151	13
α-helix	157-168	12
α-helix	174-182	9
α-helix	188-194	7
α-helix	196-198	3
α-helix	204-217	14

Chain D: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-12	11	4
α-helix	22-34	13
β-strand	37-39	3	4
β-strand	43-48	6	4
α-helix	51-53	3
β-strand	55-56	2	4
β-strand	69-79	11	4
β-strand	86-95	10	5
β-strand	98-103	6	5
β-strand	106-111	6	5
α-helix	112-114	3
β-strand	120-122	3	6
β-strand	129-131	3	6
β-strand	136-138	3	6
β-strand	142-153	12	5
β-strand	156-162	7	5
β-strand	169-170	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase II 32 kDa polypeptide	A, C	protein	187	Saccharomyces cerevisiae	P20433 (AlphaFold model)
DNA-directed RNA polymerase II 19 kDa polypeptide	B, D	protein	171	Saccharomyces cerevisiae	P34087 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1Y14_1 DNA-directed RNA polymerase II 32 kDa polypeptide (chains A, C)
LKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAV
EDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRF
RDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKEL
SNLETLY

Sequence of entity 2 (B, D), FASTA

>1Y14_2 DNA-directed RNA polymerase II 19 kDa polypeptide (chains B, D)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Primary citation

Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7. Armache, K.-J., Mitterweger, S., Meinhart, A. et al. J Biol Chem (2005) 280:7131-7134. DOI 10.1074/jbc.M413038200 · PubMed

Other PDB entries of the same protein (UniProt P20433 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SV6 1.96 Å, CryoEM structure of transcribing RNA polymerase II elongation complex with ATP and Elf1
9W8V 2.23 Å, Structure of post-translocation state of yeast Pol II complexed with a cisplatin-induced…
9QEB 2.26 Å, CryoEM structure of transcribing RNA polymerase II elongation complex
9RYB 2.33 Å, CryoEM structure of transcribing RNA polymerase II elongation complex in post-catalysis…
9KD8 2.46 Å, The structure of RNA polymerase II elongation complex paused at N-2 state by actinomycin…
9K7F 2.5 Å, RNA polymerase II elongation complex apo structure.
9W8T 2.56 Å, Structure of yeast Pol II in complex with a cisplatin-induced inter-strand crosslink…
9W8U 2.61 Å, Structure of pre-translocation state of yeast Pol II complexed with a cisplatin-induced…
9KDQ 2.63 Å, The structure of 3 ACTD bound to RNA polymerase II elongation complex with 4 CTG repeats.
24QR 2.67 Å, Structure of yeast Pol II in complex with an oxaliplatin-ICL lesion at +2 position.
9W8R 2.68 Å, Structure of yeast Pol II in complex with a short control scaffold lacking cisplatin-ICL…
8JCH 2.7 Å, Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1…

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