5T9P: Ribosome biogenesis protein 15

Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Nov 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 3,629
Mol. weight: 53.5 kDa
Released: 16 Nov 2016

Explore 5T9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T9P contains 20 α-helices and 24 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	89-96	8	5
α-helix	98-99	2
α-helix	104-112	9
β-strand	117-124	8	5
β-strand	131-139	9	5
α-helix	142-152	11
β-strand	156-157	2	6
β-strand	160-161	2	6
β-strand	163-168	6	5
α-helix	173-176	4

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	89-96	8	1
α-helix	98-99	2
α-helix	104-111	8
α-helix	112-114	3
β-strand	117-124	8	1
β-strand	131-139	9	1
α-helix	142-152	11
β-strand	156-157	2	2
β-strand	160-161	2	2
β-strand	163-168	6	1
α-helix	173-176	4
α-helix	181-186	6

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	89-96	8	3
α-helix	98-99	2
α-helix	104-112	9
β-strand	117-124	8	3
β-strand	131-139	9	3
α-helix	142-152	11
β-strand	156-157	2	4
β-strand	160-161	2	4
β-strand	163-168	6	3
α-helix	173-176	4
α-helix	181-186	6

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	89-96	8	7
α-helix	98-99	2
α-helix	104-111	8
α-helix	112-114	3
β-strand	117-124	8	7
β-strand	131-139	9	7
α-helix	143-152	10
β-strand	155-157	3	8
β-strand	160-162	3	8
β-strand	163-168	6	7
α-helix	173-176	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosome biogenesis protein 15	A, B, C, D	protein	111	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53927 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5T9P_1 Ribosome biogenesis protein 15 (chains A, B, C, D)
KDKKTLEEYSGIIYVSRLPHGFHEKELSKYFAQFGDLKEVRLARNKKTGNSRHYGFLEFV
NKEDAMIAQESMNNYLLMGHLLQVRVLPKGAKIEKLYKYKKRVLVEKGITK

Primary citation

Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate. Zhang, J., Gonzalez, L.E., Hall, T.M.T. Nucleic Acids Res (2017) 45:2829-2837. DOI 10.1093/nar/gkw961 · PubMed

Other PDB entries of the same protein (UniProt P53927 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state
7V08 2.36 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1…
7UQB 2.43 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a…
7UQZ 2.44 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a SPB1…
8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
7U0H 2.76 Å, State NE1 nucleolar 60S ribosome biogenesis intermediate - Overall model
11AA 2.78 Å, Yeast co-transcriptional pre-60S assembly intermediate Nop12 RNP
7R6Q 2.98 Å, State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region model
7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

Browse structure collections

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