3NFH: DNA-directed RNA polymerase I subunit RPA49

Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 (P4). Determined by X-ray diffraction at 2.17 Å resolution. Released 8 Sept 2010.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,587
Mol. weight: 55.43 kDa
Released: 8 Sept 2010

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

Secondary structure: helices and β-sheets

3NFH contains 34 α-helices and 12 β-strands across 2 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: 17 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	189-191	3
α-helix	198-200	3
α-helix	204-207	4
α-helix	210-213	4
α-helix	219-223	5
α-helix	227-232	6
α-helix	241-247	7
α-helix	253-255	3
α-helix	256-273	18
α-helix	280-286	7
α-helix	292-302	11
β-strand	304-305	2	1
β-strand	318-319	2	1
α-helix	322-339	18
β-strand	343-345	3	2
α-helix	346-353	8
α-helix	357-366	10
β-strand	370-373	4	2
α-helix	374-375	2
α-helix	376-382	7
α-helix	386-391	6
β-strand	393-396	4	2

Chain B: 17 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	189-191	3
α-helix	198-200	3
α-helix	204-207	4
α-helix	210-213	4
α-helix	219-223	5
α-helix	227-232	6
α-helix	241-247	7
α-helix	253-255	3
α-helix	256-273	18
β-strand	279	1	3
α-helix	280-286	7
α-helix	292-302	11
β-strand	304-305	2	4
β-strand	317	1	3
β-strand	318-319	2	4
α-helix	322-339	18
β-strand	343-345	3	5
α-helix	346-353	8
α-helix	357-366	10
β-strand	370-373	4	5
α-helix	374-375	2
α-helix	376-382	7
α-helix	386-391	6
β-strand	393-396	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase I subunit RPA49	A, B	protein	246	Saccharomyces cerevisiae	Q01080 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3NFH_1 DNA-directed RNA polymerase I subunit RPA49 (chains A, B)
MTDSAIDIVDSVRTASKDLPTRAQLDEITSNDRPTPLANIDATDVEQIYPIESIIPKKEL
QFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYE
NRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFIDPQNEDKILCYIL
AIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYK
IATMKV

Primary citation

RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex. Geiger, S.R., Lorenzen, K., Schreieck, A. et al. Mol Cell (2010) 39:583-594. DOI 10.1016/j.molcel.2010.07.028 · PubMed

Other PDB entries of the same protein (UniProt Q01080 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NFI 1.9 Å, Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49
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
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
4C3H 3.27 Å, Structure of 14-subunit RNA polymerase I at 3.27 A resolution, crystal form C2-93
9G29 3.3 Å, Yeast RNA polymerase I elongation complex stalled by an apurinic site with the…
4C3J 3.35 Å, Structure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90
5N61 3.4 Å, RNA polymerase I initially transcribing complex

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