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Subunit joining exposes nascent pre-40S rRNA for processing and quality control

Electron Microscopy
3.7Å resolution
PDB entry 6wdr coloured by chain, front view.
PDB entry 6wdr coloured by chain, side view.
PDB entry 6wdr coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero 32-mer (preferred)
Entry contents: 31 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: 40S cytosolic small ribosomal subunit and RNA
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Multimeric state: hetero 32-mer
Accessible surface area: 452984.3 Å2
Buried surface area: 150205.53 Å2
Dissociation area: 1,376.27 Å2
Dissociation energy (ΔGdiss): 3.46 kcal/mol
Dissociation entropy (TΔSdiss): 11.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-126845

Macromolecules

Small ribosomal subunit protein uS2A
Chain: A
Length: 206 amino acids
Theoretical weight: 22.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32905 (Residues: 2-207; Coverage: 82%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Pfam: Ribosomal protein S2
InterPro:
Small ribosomal subunit protein uS2A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS2A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS2A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS5
Chain: C
Length: 217 amino acids
Theoretical weight: 23.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25443 (Residues: 34-250; Coverage: 85%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Pfam:
InterPro:
Small ribosomal subunit protein uS5 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS3
Chain: D
Length: 223 amino acids
Theoretical weight: 24.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05750 (Residues: 3-225; Coverage: 93%)
Gene names: N1653, RPS3, SUF14, YNL178W
Pfam:
InterPro:
Small ribosomal subunit protein uS3 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS4A
Chain: E
Length: 260 amino acids
Theoretical weight: 29.34 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX35 (Residues: 2-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Pfam:
InterPro:
Small ribosomal subunit protein eS4A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS4A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS4A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS7
Chain: F
Length: 206 amino acids
Theoretical weight: 22.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26783 (Residues: 20-225; Coverage: 92%)
Gene names: J2045, RPS2, RPS5, YJR123W
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS6A
Chain: G
Length: 232 amino acids
Theoretical weight: 26.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX37 (Residues: 1-232; Coverage: 98%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Pfam: Ribosomal protein S6e
InterPro:
Small ribosomal subunit protein eS6A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS6A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS6A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS7A
Chain: H
Length: 184 amino acids
Theoretical weight: 21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26786 (Residues: 4-187; Coverage: 97%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Pfam: Ribosomal protein S7e
InterPro:
Small ribosomal subunit protein eS7A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS7A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS7A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS8A
Chain: I
Length: 199 amino acids
Theoretical weight: 22.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX39 (Residues: 2-200; Coverage: 100%)
Gene names: RPS14A, RPS8A, YBL06.05, YBL0613, YBL072C
Pfam: Ribosomal protein S8e
InterPro:
Small ribosomal subunit protein eS8A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS8A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS8A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS4A
Chain: J
Length: 185 amino acids
Theoretical weight: 21.21 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13516 (Residues: 2-186; Coverage: 94%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Pfam:
InterPro:
Small ribosomal subunit protein uS4A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS4A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS4A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS10A
Chain: K
Length: 96 amino acids
Theoretical weight: 11.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08745 (Residues: 1-96; Coverage: 91%)
Gene names: RPS10A, YOR293W
Pfam: Plectin/S10 domain
InterPro:
Small ribosomal subunit protein eS10A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS10A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS10A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS17A
Chain: L
Length: 140 amino acids
Theoretical weight: 16.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX47 (Residues: 6-145; Coverage: 90%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Pfam:
InterPro:
Small ribosomal subunit protein uS17A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS17A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS17A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS12
Chain: M
Length: 125 amino acids
Theoretical weight: 13.43 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P48589 (Residues: 18-142; Coverage: 87%)
Gene names: RPS12, YOR369C
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
InterPro:
Small ribosomal subunit protein eS12 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS12 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS12 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS15
Chain: N
Length: 150 amino acids
Theoretical weight: 16.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05756 (Residues: 2-151; Coverage: 99%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Pfam:
InterPro:
Small ribosomal subunit protein uS15 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS19
Chain: P
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01855 (Residues: 16-142; Coverage: 89%)
Gene names: RPS15, RPS21, YOL040C
Pfam: Ribosomal protein S19
InterPro:
Small ribosomal subunit protein uS19 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein uS9A
Chain: Q
Length: 127 amino acids
Theoretical weight: 14.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX51 (Residues: 3-129; Coverage: 89%)
Gene names: RP61R, RPS16A, YM9375.12, YMR143W
Pfam: Ribosomal protein S9/S16
InterPro:
Small ribosomal subunit protein uS9A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS9A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS9A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS17A
Chain: R
Length: 125 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02407 (Residues: 2-126; Coverage: 92%)
Gene names: RP51A, RPS17A, YML024W
Pfam: Ribosomal S17
InterPro:
Small ribosomal subunit protein eS17A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS17A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS17A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS13A
Chain: S
Length: 135 amino acids
Theoretical weight: 15.77 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX55 (Residues: 2-136; Coverage: 93%)
Gene names: D9461.35, RPS18A, YDR450W
Pfam: Ribosomal protein S13/S18
InterPro:
Small ribosomal subunit protein uS13A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS13A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS13A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS19A
Chain: T
Length: 143 amino acids
Theoretical weight: 15.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07280 (Residues: 2-144; Coverage: 99%)
Gene names: RP55A, RPS16AA, RPS19A, YOL121C
Pfam: Ribosomal protein S19e
InterPro:
Small ribosomal subunit protein eS19A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS19A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS19A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS10
Chain: U
Length: 103 amino acids
Theoretical weight: 11.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38701 (Residues: 19-121; Coverage: 85%)
Gene names: RPS20, URP2, YHL015W
Pfam: Ribosomal protein S10p/S20e
InterPro:
Small ribosomal subunit protein uS10 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS21A
Chain: V
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0V8 (Residues: 1-87; Coverage: 100%)
Gene names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Pfam: Ribosomal protein S21e
InterPro:
Small ribosomal subunit protein eS21A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS21A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS21A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS8A
Chain: W
Length: 129 amino acids
Theoretical weight: 14.52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0W1 (Residues: 2-130; Coverage: 99%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Pfam: Ribosomal protein S8
InterPro:
Small ribosomal subunit protein uS8A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS8A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS8A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS12A
Chain: X
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX29 (Residues: 2-145; Coverage: 99%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS12A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS12A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein eS24A
Chain: Y
Length: 134 amino acids
Theoretical weight: 15.23 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX31 (Residues: 2-135; Coverage: 99%)
Gene names: RPS24A, RPS24EA, YER074W
Pfam: Ribosomal protein S24e
InterPro:
Small ribosomal subunit protein eS24A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS24A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS24A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS25A
Chain: Z
Length: 63 amino acids
Theoretical weight: 7.28 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E792 (Residues: 42-104; Coverage: 58%)
Gene names: RPS25A, RPS31A, YGR027C
Pfam: S25 ribosomal protein
InterPro:
Small ribosomal subunit protein eS25A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS25A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS25A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS27A
Chain: b
Length: 81 amino acids
Theoretical weight: 8.76 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35997 (Residues: 2-82; Coverage: 99%)
Gene names: RPS27A, YKL156W
Pfam: Ribosomal protein S27
InterPro:
Small ribosomal subunit protein eS27A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS27A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS27A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS28A
Chain: c
Length: 63 amino acids
Theoretical weight: 7.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E7X9 (Residues: 5-67; Coverage: 94%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Pfam: Ribosomal protein S28e
InterPro:
Small ribosomal subunit protein eS28A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS28A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS28A in PDB entry 6wdr, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS14A
Chain: d
Length: 37 amino acids
Theoretical weight: 4.37 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41057 (Residues: 20-56; Coverage: 66%)
Gene names: L8084.11, RPS29A, RPS36A, YLR388W, YS29A
Pfam: Ribosomal protein S14p/S29e
InterPro:
Small ribosomal subunit protein uS14A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein uS14A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein uS14A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS30A
Chain: e
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX33 (Residues: 1-63; Coverage: 100%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Pfam: Ribosomal protein S30
InterPro: Small ribosomal subunit protein eS30
Small ribosomal subunit protein eS30A in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS30A in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS30A in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein eS31
Chain: f
Length: 71 amino acids
Theoretical weight: 8.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05759 (Residues: 82-152; Coverage: 47%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Pfam: Ribosomal protein S27a
InterPro:
Small ribosomal subunit protein eS31 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein eS31 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein eS31 in PDB entry 6wdr, assembly 1, top view.
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Small ribosomal subunit protein RACK1
Chain: g
Length: 317 amino acids
Theoretical weight: 34.64 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38011 (Residues: 3-319; Coverage: 99%)
Gene names: ASC1, CPC2, YM9718.15C, YMR116C
Pfam: WD domain, G-beta repeat
InterPro:
Small ribosomal subunit protein RACK1 in PDB entry 6wdr, assembly 1, front view.
Small ribosomal subunit protein RACK1 in PDB entry 6wdr, assembly 1, side view.
Small ribosomal subunit protein RACK1 in PDB entry 6wdr, assembly 1, top view.
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Ribosome biogenesis protein TSR1
Chain: k
Length: 788 amino acids
Theoretical weight: 90.88 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07381 (Residues: 1-788; Coverage: 100%)
Gene names: TSR1, YDL060W
Pfam:
InterPro:
Ribosome biogenesis protein TSR1 in PDB entry 6wdr, assembly 1, front view.
Ribosome biogenesis protein TSR1 in PDB entry 6wdr, assembly 1, side view.
Ribosome biogenesis protein TSR1 in PDB entry 6wdr, assembly 1, top view.
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RNA chain 2
Name: 20S ribosomal RNA
Representative chains: 2
Length: 1910 nucleotides
Theoretical weight: 614.94 KDa
Rfam: Eukaryotic small subunit ribosomal RNA
20S ribosomal RNA in PDB entry 6wdr, assembly 1, front view.
20S ribosomal RNA in PDB entry 6wdr, assembly 1, side view.
20S ribosomal RNA in PDB entry 6wdr, assembly 1, top view.
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