1DZF: RPB5 from S.cerevisiae

RPB5 from S.cerevisiae. Determined by X-ray diffraction at 1.9 Å resolution. Released 9 Jun 2000.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 1
Atoms: 1,894
Mol. weight: 25.12 kDa
Released: 9 Jun 2000

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

Secondary structure: helices and β-sheets

1DZF contains 13 α-helices and 14 β-strands across 1 chain. 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: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
β-strand	28	1	1
α-helix	32-35	4
α-helix	39-46	8
β-strand	47	1	2
β-strand	53	1	2
α-helix	55-57	3
β-strand	60-62	3	3
β-strand	64	1	1
α-helix	66-71	6
β-strand	78-82	5	3
β-strand	87-88	2	4
α-helix	90-102	13
β-strand	107-112	6	3
β-strand	115-116	2	4
α-helix	118-121	4
β-strand	131-136	6	3
α-helix	137-140	4
α-helix	144-146	3
β-strand	152-155	4	5
α-helix	156-157	2
α-helix	158-167	10
α-helix	172-174	3
β-strand	177-178	2	5
α-helix	183-188	6
β-strand	195-199	5	5
β-strand	210-214	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerases I, II, and III subunit rpabc 1	A	protein	215	SACCHAROMYCES CEREVISIAE	P20434 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1DZF_1 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 (chains A)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Primary citation

Crystal Structure of Rpb5, a Universal Eukaryotic RNA Polymerase Subunit and Transcription Factor Interaction Target. Todone, F., Weinzierl, R.O.J., Brick, P. et al. Proc Natl Acad Sci U S A (2000) 97:6306. DOI 10.1073/PNAS.97.12.6306 · PubMed

Other PDB entries of the same protein (UniProt P20434 (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
1TWF 2.3 Å, RNA polymerase II complexed with UTP at 2.3 A resolution
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.
30ES 2.54 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
30EP 2.55 Å, Cryo-EM structure of the yeast RNA polymerase II elongation complex with 19-mer RNA in…
9W8T 2.56 Å, Structure of yeast Pol II in complex with a cisplatin-induced inter-strand crosslink…
7Z0H 2.6 Å, Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.6 A (focus subunit AC40).
9W8U 2.61 Å, Structure of pre-translocation state of yeast Pol II complexed with a cisplatin-induced…

Browse structure collections

About this viewer

MolViewer shows 1DZF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.