› 6eml

Electron Microscopy
3.6Å resolution

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae

Released:
DOI: 10.2210/pdb6eml/pdb
PDB entry 6eml coloured by chain, front view.
PDB entry 6eml coloured by chain, side view.
PDB entry 6eml coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae.
Heuer A, Thomson E, Schmidt C, Berninghausen O, Becker T, Hurt E, Beckmann R
Elife 6 (2017)
PMID: 29155690
Related structures: EMD-3886

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
PDBe Complex ID:
PDB-CPX-126848 (preferred)
Entry contents:
31 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (32 distinct):
Small ribosomal subunit protein eS12 Chain: D
Molecule details ›
Chain: D
Length: 143 amino acids
Theoretical weight: 15.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P48589 (Residues: 1-143; Coverage: 100%)
Gene names: RPS12, YOR369C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Small ribosomal subunit protein uS7 Chain: B
Molecule details ›
Chain: B
Length: 225 amino acids
Theoretical weight: 25.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26783 (Residues: 1-225; Coverage: 100%)
Gene names: J2045, RPS2, RPS5, YJR123W
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
Small ribosomal subunit protein eS17A Chain: C
Molecule details ›
Chain: C
Length: 136 amino acids
Theoretical weight: 15.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P02407 (Residues: 1-136; Coverage: 100%)
Gene names: RP51A, RPS17A, YML024W
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS19 Chain: E
Molecule details ›
Chain: E
Length: 142 amino acids
Theoretical weight: 16.03 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q01855 (Residues: 1-142; Coverage: 100%)
Gene names: RPS15, RPS21, YOL040C
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9A Chain: F
Molecule details ›
Chain: F
Length: 143 amino acids
Theoretical weight: 15.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX51 (Residues: 1-143; Coverage: 100%)
Gene names: RP61R, RPS16A, YM9375.12, YMR143W
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
Small ribosomal subunit protein uS13A Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 17.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX55 (Residues: 1-146; Coverage: 100%)
Gene names: D9461.35, RPS18A, YDR450W
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19A Chain: I
Molecule details ›
Chain: I
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07280 (Residues: 1-144; Coverage: 100%)
Gene names: RP55A, RPS16AA, RPS19A, YOL121C
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein eS25A Chain: K
Molecule details ›
Chain: K
Length: 108 amino acids
Theoretical weight: 12.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q3E792 (Residues: 1-108; Coverage: 100%)
Gene names: RPS25A, RPS31A, YGR027C
Sequence domains: S25 ribosomal protein
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Small ribosomal subunit protein eS28B Chain: L
Molecule details ›
Chain: L
Length: 67 amino acids
Theoretical weight: 7.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0X0 (Residues: 1-67; Coverage: 100%)
Gene names: L8479.5, RPS28B, RPS33B, YLR264W
Sequence domains: Ribosomal protein S28e
Structure domains: Nucleic acid-binding proteins
Ubiquitin-ribosomal protein eS31 fusion protein Chain: N
Molecule details ›
Chain: N
Length: 152 amino acids
Theoretical weight: 17.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05759 (Residues: 1-152; Coverage: 100%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains:
Small ribosomal subunit protein uS2A Chain: P
Molecule details ›
Chain: P
Length: 252 amino acids
Theoretical weight: 28.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32905 (Residues: 1-252; Coverage: 100%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Sequence domains: Ribosomal protein S2
Structure domains: Glucose-6-phosphate isomerase like protein; domain 1
Small ribosomal subunit protein eS1A Chain: Q
Molecule details ›
Chain: Q
Length: 255 amino acids
Theoretical weight: 28.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33442 (Residues: 1-255; Coverage: 100%)
Gene names: L9753.9, PLC1, RPS10A, RPS1A, YLR441C
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chain: R
Molecule details ›
Chain: R
Length: 254 amino acids
Theoretical weight: 27.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25443 (Residues: 1-254; Coverage: 100%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Sequence domains:
Structure domains:
Small ribosomal subunit protein eS4A Chain: S
Molecule details ›
Chain: S
Length: 261 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX35 (Residues: 1-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Sequence domains:
Structure domains:
Small ribosomal subunit protein eS6A Chain: T
Molecule details ›
Chain: T
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX37 (Residues: 1-236; Coverage: 100%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7A Chain: U
Molecule details ›
Chain: U
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P26786 (Residues: 1-190; Coverage: 100%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8A Chain: V
Molecule details ›
Chain: V
Length: 200 amino acids
Theoretical weight: 22.54 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX39 (Residues: 1-200; Coverage: 100%)
Gene names: RPS14A, RPS8A, YBL06.05, YBL0613, YBL072C
Sequence domains: Ribosomal protein S8e
Structure domains: Ribosomal protein S8e, subdomain
Small ribosomal subunit protein uS4A Chain: W
Molecule details ›
Chain: W
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: O13516 (Residues: 1-197; Coverage: 100%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein uS17A Chain: X
Molecule details ›
Chain: X
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX47 (Residues: 1-156; Coverage: 100%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Small ribosomal subunit protein uS15 Chain: Y
Molecule details ›
Chain: Y
Length: 151 amino acids
Theoretical weight: 17.06 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P05756 (Residues: 1-151; Coverage: 100%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains:
Structure domains: S15/NS1, RNA-binding
Small ribosomal subunit protein uS11A Chain: Z
Molecule details ›
Chain: Z
Length: 137 amino acids
Theoretical weight: 14.56 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P06367 (Residues: 1-137; Coverage: 100%)
Gene names: CRY1, RPL59, RPS14A, YCR031C, YCR31C
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Small ribosomal subunit protein eS21A Chain: a
Molecule details ›
Chain: a
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0V8 (Residues: 1-87; Coverage: 100%)
Gene names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Sequence domains: Ribosomal protein S21e
Structure domains: Hypothetical Cytosolic Protein; Chain: A;
Small ribosomal subunit protein uS8A Chain: b
Molecule details ›
Chain: b
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C0W1 (Residues: 1-130; Coverage: 100%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Sequence domains: Ribosomal protein S8
Structure domains:
Small ribosomal subunit protein uS12A Chain: c
Molecule details ›
Chain: c
Length: 145 amino acids
Theoretical weight: 16.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX29 (Residues: 1-145; Coverage: 100%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24A Chain: d
Molecule details ›
Chain: d
Length: 135 amino acids
Theoretical weight: 15.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX31 (Residues: 1-135; Coverage: 100%)
Gene names: RPS24A, RPS24EA, YER074W
Sequence domains: Ribosomal protein S24e
Structure domains: Alpha-Beta Plaits
Small ribosomal subunit protein eS27A Chain: f
Molecule details ›
Chain: f
Length: 82 amino acids
Theoretical weight: 8.89 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P35997 (Residues: 1-82; Coverage: 100%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Structure domains: Zn-binding ribosomal proteins
Ribosome biogenesis protein TSR1 Chain: t
Molecule details ›
Chain: t
Length: 788 amino acids
Theoretical weight: 90.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07381 (Residues: 1-788; Coverage: 100%)
Gene names: TSR1, YDL060W
Sequence domains:
Small ribosomal subunit protein eS30A Chain: g
Molecule details ›
Chain: g
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0CX33 (Residues: 1-63; Coverage: 100%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Sequence domains: Ribosomal protein S30
Pre-rRNA-processing protein PNO1 Chain: p
Molecule details ›
Chain: p
Length: 274 amino acids
Theoretical weight: 30.38 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q99216 (Residues: 1-274; Coverage: 100%)
Gene names: DIM2, O3513, PNO1, RRP20, YOR145C, YOR3513C
Sequence domains: Krr1 KH1 domain
Serine/threonine-protein kinase RIO2 Chain: r
Molecule details ›
Chain: r
Length: 425 amino acids
Theoretical weight: 49.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40160 (Residues: 1-425; Coverage: 100%)
Gene names: N1342, RIO2, YNL207W
Sequence domains:
Essential nuclear protein 1 Chain: e
Molecule details ›
Chain: e
Length: 483 amino acids
Theoretical weight: 55.21 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38333 (Residues: 1-483; Coverage: 100%)
Gene names: ENP1, MEG1, YBR1635, YBR247C
Sequence domains: Bystin
pre-18S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1800 nucleotides
Theoretical weight: 579.76 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-3886

Quick links

Citations

11 review citations

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

7 mentions without citation

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae.
Heuer et al. (2017)
6 more