2RF4: RNA Polymerase I subcomplex A14/43

Crystal structure of the RNA Polymerase I subcomplex A14/43. Determined by X-ray diffraction at 3.1 Å resolution. Released 15 Jan 2008.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 5,530
Mol. weight: 101.7 kDa
Released: 15 Jan 2008

Explore 2RF4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2RF4 contains 24 α-helices and 53 β-strands across 6 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: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-29	2	1
β-strand	34-35	2	1
β-strand	38-48	11	2
α-helix	51-53	3
α-helix	57-69	13
β-strand	70	1	2
β-strand	73-74	2	2
β-strand	79-88	10	2
β-strand	115-125	11	2
β-strand	132-137	6	3
β-strand	145-149	5	3
β-strand	153-157	5	3
β-strand	167	1	4
β-strand	218	1	4
β-strand	224	1	4
β-strand	228-239	12	3
β-strand	241-248	8	3

Chains B and D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21-24	4	2
β-strand	29-30	2	2
α-helix	31-32	2
α-helix	33-48	16
α-helix	82-98	17

Chain C: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	26-27	2
β-strand	28	1	5
α-helix	34	1
β-strand	35	1	5
α-helix	36	1
β-strand	38-47	10	6
α-helix	51-53	3
α-helix	58-61	4
α-helix	66-69	4
β-strand	70	1	6
β-strand	73-74	2	6
β-strand	79-88	10	6
α-helix	89-91	3
β-strand	116-125	10	6
β-strand	132-137	6	7
β-strand	145-149	5	7
β-strand	153-157	5	7
α-helix	159-161	3
β-strand	167	1	8
β-strand	218	1	8
β-strand	224	1	8
β-strand	228-239	12	7
β-strand	241-248	8	7

Chain E: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	26-27	2
β-strand	28-29	2	9
β-strand	34-35	2	9
β-strand	38-47	10	10
α-helix	51-53	3
α-helix	58-69	12
β-strand	70	1	10
β-strand	73-74	2	10
β-strand	79-88	10	10
β-strand	116-125	10	10
β-strand	132-140	9	11
β-strand	145-149	5	11
β-strand	153-157	5	11
β-strand	167	1	12
β-strand	170-171	2	13
β-strand	211-215	5	13
β-strand	218	1	12
β-strand	224	1	12
β-strand	228-239	12	11
β-strand	241-248	8	11

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-20	2
β-strand	21-24	4	10
β-strand	29-30	2	10
α-helix	31-32	2
α-helix	33-48	16
α-helix	82-98	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase I subunit RPA4	A, C, E	protein	214	Saccharomyces cerevisiae	P46669 (AlphaFold model)
DNA-directed RNA polymerase I subunit RPA4	B, D, F	protein	87	Saccharomyces cerevisiae	P50106 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>2RF4_1 DNA-directed RNA polymerase I subunit RPA4 (chains A, C, E)
MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQG
VMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHV
NLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHW
VDSNGEPIDGKLRFTVRNVHTTGRVVSVDGTLIS

Sequence of entity 2 (B, D, F), FASTA

>2RF4_2 DNA-directed RNA polymerase I subunit RPA4 (chains B, D, F)
MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDIDTNLSSS
ISQLKRIQRDFKGLPPAQDFSAAPIQV

Primary citation

Functional architecture of RNA polymerase I. Kuhn, C.D., Geiger, S.R., Baumli, S. et al. Cell (2007) 131:1260-1272. DOI 10.1016/j.cell.2007.10.051 · PubMed

Other PDB entries of the same protein (UniProt P46669 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RUI 2.7 Å, RNA Polymerase I Pre-initiation complex DNA opening intermediate 2
9G1V 2.7 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site
4C2M 2.8 Å, Structure of RNA polymerase I at 2.8 A resolution
9G27 2.8 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site, pre-translocation…
6RQL 2.9 Å, RNA Polymerase I Closed Conformation 2 (CC2)
4C3I 3.0 Å, Structure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100
6RWE 3.0 Å, RNA Polymerase I Open Complex conformation 2
6RRD 3.1 Å, RNA Polymerase I Pre-initiation complex DNA opening intermediate 1
6HLQ 3.18 Å, Yeast RNA polymerase I* elongation complex bound to nucleotide analog GMPCPP
6HLR 3.18 Å, Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (core focused)
9G2B 3.2 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site, 12-subunit
6HLS 3.21 Å, Yeast apo RNA polymerase I*

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