› 5wlc

Electron Microscopy
3.8Å resolution

The complete structure of the small subunit processome

Released:
DOI: 10.2210/pdb5wlc/pdb
PDB entry 5wlc coloured by chain, front view.
PDB entry 5wlc coloured by chain, side view.
PDB entry 5wlc coloured by chain, top view.
Source organism: Saccharomyces cerevisiae BY4741
Primary publication:
The complete structure of the small-subunit processome.
Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S
Nat Struct Mol Biol 24 944-953 (2017)
PMID: 28945246
Related structures: EMD-8859

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + pseudouridine(1191) in yeast 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1191) in yeast 18S rRNA
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 70-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-495810 (preferred)
Entry contents:
63 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (66 distinct):
Small ribosomal subunit protein uS13A Chain: L3
Molecule details ›
Chain: L3
Length: 146 amino acids
Theoretical weight: 16.77 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein eS4A Chain: L4
Molecule details ›
Chain: L4
Length: 261 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae BY4741
Rps5p Chain: L5
Molecule details ›
Chain: L5
Length: 225 amino acids
Theoretical weight: 25.07 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein eS6A Chain: L6
Molecule details ›
Chain: L6
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein eS7A Chain: L7
Molecule details ›
Chain: L7
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein eS8A Chain: L8
Molecule details ›
Chain: L8
Length: 200 amino acids
Theoretical weight: 22.54 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS4A Chain: L9
Molecule details ›
Chain: L9
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS9A Chain: LC
Molecule details ›
Chain: LC
Length: 143 amino acids
Theoretical weight: 15.88 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS17A Chain: LD
Molecule details ›
Chain: LD
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS8A Chain: LE
Molecule details ›
Chain: LE
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein eS24A Chain: LF
Molecule details ›
Chain: LF
Length: 135 amino acids
Theoretical weight: 15.36 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein eS28A Chain: LG
Molecule details ›
Chain: LG
Length: 67 amino acids
Theoretical weight: 7.61 KDa
Source organism: Saccharomyces cerevisiae BY4741
NET1-associated nuclear protein 1 Chain: LH
Molecule details ›
Chain: LH
Length: 896 amino acids
Theoretical weight: 100.96 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 8 Chain: LI
Molecule details ›
Chain: LI
Length: 713 amino acids
Theoretical weight: 65.57 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 15 Chain: LJ
Molecule details ›
Chain: LJ
Length: 513 amino acids
Theoretical weight: 57.77 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 9 Chain: LK
Molecule details ›
Chain: LK
Length: 575 amino acids
Theoretical weight: 64.38 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 5 Chain: LL
Molecule details ›
Chain: LL
Length: 643 amino acids
Theoretical weight: 72.08 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 10 Chain: LM
Molecule details ›
Chain: LM
Length: 1769 amino acids
Theoretical weight: 200.02 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 4 Chain: LN
Molecule details ›
Chain: LN
Length: 776 amino acids
Theoretical weight: 87.32 KDa
Source organism: Saccharomyces cerevisiae BY4741
Periodic tryptophan protein 2 Chain: LO
Molecule details ›
Chain: LO
Length: 923 amino acids
Theoretical weight: 104.1 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 6 Chain: LP
Molecule details ›
Chain: LP
Length: 440 amino acids
Theoretical weight: 48.44 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 12 Chain: LQ
Molecule details ›
Chain: LQ
Length: 943 amino acids
Theoretical weight: 105.04 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 13 Chain: LR
Molecule details ›
Chain: LR
Length: 817 amino acids
Theoretical weight: 75.04 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 18 Chain: LS
Molecule details ›
Chain: LS
Length: 594 amino acids
Theoretical weight: 66.49 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 21 Chain: LT
Molecule details ›
Chain: LT
Length: 939 amino acids
Theoretical weight: 104.93 KDa
Source organism: Saccharomyces cerevisiae BY4741
Protein SOF1 Chain: LU
Molecule details ›
Chain: LU
Length: 489 amino acids
Theoretical weight: 56.89 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosome biogenesis protein ENP2 Chain: LV
Molecule details ›
Chain: LV
Length: 707 amino acids
Theoretical weight: 81.86 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 7 Chain: LW
Molecule details ›
Chain: LW
Length: 554 amino acids
Theoretical weight: 62.42 KDa
Source organism: Saccharomyces cerevisiae BY4741
RNA cytidine acetyltransferase Chains: LX, LY
Molecule details ›
Chains: LX, LY
Length: 1056 amino acids
Theoretical weight: 95.34 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar ribonucleoprotein protein IMP3 Chain: LZ
Molecule details ›
Chain: LZ
Length: 183 amino acids
Theoretical weight: 21.93 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein MPP10 Chain: NA
Molecule details ›
Chain: NA
Length: 593 amino acids
Theoretical weight: 67.04 KDa
Source organism: Saccharomyces cerevisiae BY4741
Something about silencing protein 10 Chain: NB
Molecule details ›
Chain: NB
Length: 610 amino acids
Theoretical weight: 69.71 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar ribonucleoprotein protein LCP5 Chain: NC
Molecule details ›
Chain: NC
Length: 357 amino acids
Theoretical weight: 40.86 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 16 Chain: ND
Molecule details ›
Chain: ND
Length: 214 amino acids
Theoretical weight: 23.84 KDa
Source organism: Saccharomyces cerevisiae BY4741
Protein FAF1 Chain: NE
Molecule details ›
Chain: NE
Length: 346 amino acids
Theoretical weight: 38.17 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS15 Chain: NF
Molecule details ›
Chain: NF
Length: 151 amino acids
Theoretical weight: 17.06 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS11A Chain: NG
Molecule details ›
Chain: NG
Length: 137 amino acids
Theoretical weight: 14.56 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 22 Chain: NH
Molecule details ›
Chain: NH
Length: 1237 amino acids
Theoretical weight: 140.66 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosomal RNA-processing protein 7 Chain: NI
Molecule details ›
Chain: NI
Length: 297 amino acids
Theoretical weight: 34.53 KDa
Source organism: Saccharomyces cerevisiae BY4741
rRNA biogenesis protein RRP5 Chain: NJ
Molecule details ›
Chain: NJ
Length: 1729 amino acids
Theoretical weight: 193.41 KDa
Source organism: Saccharomyces cerevisiae BY4741
KRR1 small subunit processome component Chain: NK
Molecule details ›
Chain: NK
Length: 316 amino acids
Theoretical weight: 37.23 KDa
Source organism: Saccharomyces cerevisiae BY4741
Nucleolar protein 56 Chain: SA
Molecule details ›
Chain: SA
Length: 504 amino acids
Theoretical weight: 56.39 KDa
Source organism: Saccharomyces cerevisiae BY4741
Nucleolar protein 58 Chain: SB
Molecule details ›
Chain: SB
Length: 511 amino acids
Theoretical weight: 53.81 KDa
Source organism: Saccharomyces cerevisiae BY4741
rRNA 2'-O-methyltransferase fibrillarin Chains: SC, SD
Molecule details ›
Chains: SC, SD
Length: 327 amino acids
Theoretical weight: 34.53 KDa
Source organism: Saccharomyces cerevisiae BY4741
13 kDa ribonucleoprotein-associated protein Chains: SE, SF
Molecule details ›
Chains: SE, SF
Length: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosomal RNA-processing protein 9 Chain: SG
Molecule details ›
Chain: SG
Length: 573 amino acids
Theoretical weight: 65.15 KDa
Source organism: Saccharomyces cerevisiae BY4741
RNA 3'-terminal phosphate cyclase-like protein Chain: SH
Molecule details ›
Chain: SH
Length: 367 amino acids
Theoretical weight: 40.22 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosome biogenesis protein BMS1 Chain: SI
Molecule details ›
Chain: SI
Length: 1184 amino acids
Theoretical weight: 135.15 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosomal RNA small subunit methyltransferase NEP1 Chains: SJ, SK
Molecule details ›
Chains: SJ, SK
Length: 252 amino acids
Theoretical weight: 27.94 KDa
Source organism: Saccharomyces cerevisiae BY4741
rRNA-processing protein FCF1 Chain: SL
Molecule details ›
Chain: SL
Length: 189 amino acids
Theoretical weight: 21.65 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar ribonucleoprotein protein IMP4 Chain: SM
Molecule details ›
Chain: SM
Length: 290 amino acids
Theoretical weight: 33.54 KDa
Source organism: Saccharomyces cerevisiae BY4741
Ribosome biogenesis protein UTP30 Chain: SN
Molecule details ›
Chain: SN
Length: 274 amino acids
Theoretical weight: 31.67 KDa
Source organism: Saccharomyces cerevisiae BY4741
Pre-rRNA-processing protein PNO1 Chain: SO
Molecule details ›
Chain: SO
Length: 274 amino acids
Theoretical weight: 30.38 KDa
Source organism: Saccharomyces cerevisiae BY4741
Utp20 Chain: SP
Molecule details ›
Chain: SP
Length: 982 amino acids
Theoretical weight: 83.59 KDa
Source organism: Saccharomyces cerevisiae BY4741
rRNA-processing protein FCF2 Chain: SQ
Molecule details ›
Chain: SQ
Length: 217 amino acids
Theoretical weight: 25.69 KDa
Source organism: Saccharomyces cerevisiae BY4741
Small ribosomal subunit protein uS12A Chain: SR
Molecule details ›
Chain: SR
Length: 145 amino acids
Theoretical weight: 16.07 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 14 Chain: SS
Molecule details ›
Chain: SS
Length: 898 amino acids
Theoretical weight: 101.1 KDa
Source organism: Saccharomyces cerevisiae BY4741
Nucleolar complex protein 14 Chain: ST
Molecule details ›
Chain: ST
Length: 792 amino acids
Theoretical weight: 85.99 KDa
Source organism: Saccharomyces cerevisiae BY4741
Nucleolar complex protein 4 Chain: SU
Molecule details ›
Chain: SU
Length: 552 amino acids
Theoretical weight: 58.37 KDa
Source organism: Saccharomyces cerevisiae BY4741
Regulator of rDNA transcription 14 Chain: SV
Molecule details ›
Chain: SV
Length: 206 amino acids
Theoretical weight: 21.04 KDa
Source organism: Saccharomyces cerevisiae BY4741
Unassigned peptides Chain: SX
Molecule details ›
Chain: SX
Length: 103 amino acids
Theoretical weight: 8.78 KDa
Source organism: Saccharomyces cerevisiae BY4741
U3 small nucleolar RNA-associated protein 11 Chain: SY
Molecule details ›
Chain: SY
Length: 250 amino acids
Theoretical weight: 29.81 KDa
Source organism: Saccharomyces cerevisiae BY4741
Essential nuclear protein 1 Chain: SZ
Molecule details ›
Chain: SZ
Length: 483 amino acids
Theoretical weight: 55.21 KDa
Source organism: Saccharomyces cerevisiae BY4741
5' ETS Chain: L0
Molecule details ›
Chain: L0
Length: 700 nucleotides
Theoretical weight: 225.54 KDa
Source organism: Saccharomyces cerevisiae BY4741
18S pre-rRNA Chain: L1
Molecule details ›
Chain: L1
Length: 1807 nucleotides
Theoretical weight: 582.05 KDa
Source organism: Saccharomyces cerevisiae BY4741
Sequence domains: Eukaryotic small subunit ribosomal RNA
U3 snoRNA Chain: L2
Molecule details ›
Chain: L2
Length: 333 nucleotides
Theoretical weight: 106.5 KDa
Source organism: Saccharomyces cerevisiae BY4741
Sequence domains: Fungal small nucleolar RNA U3

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-8859

Quick links

Citations

17 review citations

Eukaryotic Ribosome Assembly.
Baßler et al. (2019)
16 more

23 mentions without citation

Ribosome assembly coming into focus.
Klinge et al. (2019)
22 more