› 5tzs

Electron Microscopy
5.1Å resolution

Architecture of the yeast small subunit processome

Released:
DOI: 10.2210/pdb5tzs/pdb
PDB entry 5tzs coloured by chain, front view.
PDB entry 5tzs coloured by chain, side view.
PDB entry 5tzs coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Architecture of the yeast small subunit processome.
Chaker-Margot M, Barandun J, Hunziker M, Klinge S
Science 355 (2017)
PMID: 27980088
Related structures: EMD-8473

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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119181 (preferred)
Entry contents:
47 distinct polypeptide molecules
3 distinct DNA molecules
3 distinct RNA molecules
Macromolecules (53 distinct):
Small ribosomal subunit protein eS6A Chain: 3
Molecule details ›
Chain: 3
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 eS4A Chain: 5
Molecule details ›
Chain: 5
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:
Small ribosomal subunit protein uS7 Chain: 6
Molecule details ›
Chain: 6
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
Small ribosomal subunit protein eS7A Chain: 7
Molecule details ›
Chain: 7
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: 8
Molecule details ›
Chain: 8
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
Small ribosomal subunit protein uS4A Chain: 9
Molecule details ›
Chain: 9
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 uS9A Chain: C
Molecule details ›
Chain: C
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
Small ribosomal subunit protein uS17A Chain: D
Molecule details ›
Chain: D
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:
Small ribosomal subunit protein uS8A Chain: E
Molecule details ›
Chain: E
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
Small ribosomal subunit protein eS24A Chain: F
Molecule details ›
Chain: F
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
Small ribosomal subunit protein eS28A Chain: G
Molecule details ›
Chain: G
Length: 67 amino acids
Theoretical weight: 7.62 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q3E7X9 (Residues: 1-67; Coverage: 100%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Sequence domains: Ribosomal protein S28e
Utp4 Chain: H
Molecule details ›
Chain: H
Length: 544 amino acids
Theoretical weight: 46.32 KDa
Source organism: Saccharomyces cerevisiae S288C
UtpA_CTD1 Chain: I
Molecule details ›
Chain: I
Length: 176 amino acids
Theoretical weight: 15 KDa
Source organism: Saccharomyces cerevisiae S288C
UtpA_CTD2 Chains: J, K
Molecule details ›
Chains: J, K
Length: 107 amino acids
Theoretical weight: 9.12 KDa
Source organism: Saccharomyces cerevisiae S288C
Beta-propeller 2 Chain: M
Molecule details ›
Chain: M
Length: 258 amino acids
Theoretical weight: 21.97 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp17 Chain: N
Molecule details ›
Chain: N
Length: 545 amino acids
Theoretical weight: 46.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp1 Chain: O
Molecule details ›
Chain: O
Length: 638 amino acids
Theoretical weight: 54.32 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp6 Chain: P
Molecule details ›
Chain: P
Length: 306 amino acids
Theoretical weight: 26.06 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp12 Chain: Q
Molecule details ›
Chain: Q
Length: 710 amino acids
Theoretical weight: 60.44 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp13 Chain: R
Molecule details ›
Chain: R
Length: 717 amino acids
Theoretical weight: 61.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp18 Chain: S
Molecule details ›
Chain: S
Length: 250 amino acids
Theoretical weight: 21.29 KDa
Source organism: Saccharomyces cerevisiae S288C
U3 small nucleolar RNA-associated protein 21 Chain: T
Molecule details ›
Chain: T
Length: 781 amino acids
Theoretical weight: 83.44 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06078 (Residues: 21-673; Coverage: 70%)
Gene names: L8084.22, UTP21, YLR409C
Sequence domains: WD domain, G-beta repeat
Beta-propeller 5 Chain: U
Molecule details ›
Chain: U
Length: 284 amino acids
Theoretical weight: 24.19 KDa
Source organism: Saccharomyces cerevisiae S288C
Enp2 Chain: V
Molecule details ›
Chain: V
Length: 263 amino acids
Theoretical weight: 22.4 KDa
Source organism: Saccharomyces cerevisiae S288C
UtpA_CTD4 Chain: W
Molecule details ›
Chain: W
Length: 104 amino acids
Theoretical weight: 8.87 KDa
Source organism: Saccharomyces cerevisiae S288C
Kre33 Chain: X
Molecule details ›
Chain: X
Length: 640 amino acids
Theoretical weight: 54.49 KDa
Source organism: Saccharomyces cerevisiae S288C
Kre33 Chain: Y
Molecule details ›
Chain: Y
Length: 641 amino acids
Theoretical weight: 54.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Imp3 Chain: Z
Molecule details ›
Chain: Z
Length: 151 amino acids
Theoretical weight: 12.87 KDa
Source organism: Saccharomyces cerevisiae S288C
Nop56 Chain: a
Molecule details ›
Chain: a
Length: 312 amino acids
Theoretical weight: 26.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Nop58 Chain: b
Molecule details ›
Chain: b
Length: 341 amino acids
Theoretical weight: 29.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Nop1 Chain: c
Molecule details ›
Chain: c
Length: 221 amino acids
Theoretical weight: 18.83 KDa
Source organism: Saccharomyces cerevisiae S288C
Nop1 Chain: d
Molecule details ›
Chain: d
Length: 216 amino acids
Theoretical weight: 18.4 KDa
Source organism: Saccharomyces cerevisiae S288C
13 kDa ribonucleoprotein-associated protein Chains: e, f
Molecule details ›
Chains: e, f
Length: 126 amino acids
Theoretical weight: 13.58 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P39990 (Residues: 1-126; Coverage: 100%)
Gene names: SNU13, YEL026W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal RNA-processing protein 9 Chain: g
Molecule details ›
Chain: g
Length: 573 amino acids
Theoretical weight: 65.15 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06506 (Residues: 1-573; Coverage: 100%)
Gene names: RRP9, YPR137W
Sequence domains: WD domain, G-beta repeat
RNA 3'-terminal phosphate cyclase-like protein Chain: h
Molecule details ›
Chain: h
Length: 367 amino acids
Theoretical weight: 40.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08096 (Residues: 1-367; Coverage: 100%)
Gene names: RCL1, RTC1, YOL010W
Sequence domains:
Ribosome biogenesis protein BMS1 Chain: i
Molecule details ›
Chain: i
Length: 511 amino acids
Theoretical weight: 46.6 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08965 (Residues: 546-636; Coverage: 8%)
Gene names: BMS1, YPL217C
Ribosomal RNA small subunit methyltransferase NEP1 Chains: j, k
Molecule details ›
Chains: j, k
Length: 252 amino acids
Theoretical weight: 27.94 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06287 (Residues: 1-252; Coverage: 100%)
Gene names: EMG1, L9470.5, NEP1, YLR186W
Sequence domains: EMG1/NEP1 methyltransferase
Utp24 Chain: l
Molecule details ›
Chain: l
Length: 124 amino acids
Theoretical weight: 10.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Imp4 Chain: m
Molecule details ›
Chain: m
Length: 156 amino acids
Theoretical weight: 13.29 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp30 Chain: n
Molecule details ›
Chain: n
Length: 160 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Unassigned KH domain Chain: o
Molecule details ›
Chain: o
Length: 175 amino acids
Theoretical weight: 14.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Utp20 Chain: p
Molecule details ›
Chain: p
Length: 924 amino acids
Theoretical weight: 78.65 KDa
Source organism: Saccharomyces cerevisiae S288C
Repeat protein 2 Chain: q
Molecule details ›
Chain: q
Length: 372 amino acids
Theoretical weight: 31.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS12A Chain: r
Molecule details ›
Chain: r
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
Beta-propeller 1 Chains: s, t, u
Molecule details ›
Chains: s, t, u
Length: 290 amino acids
Theoretical weight: 24.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Repeat protein 1 Chain: v
Molecule details ›
Chain: v
Length: 580 amino acids
Theoretical weight: 49.38 KDa
Source organism: Saccharomyces cerevisiae S288C
Unassigned protein helices Chain: y
Molecule details ›
Chain: y
Length: 507 amino acids
Theoretical weight: 43.17 KDa
Source organism: Saccharomyces cerevisiae S288C
5' domain-associated Chain: A
Molecule details ›
Chain: A
Length: 39 nucleotides
Theoretical weight: 7.6 KDa
3' domain-associated Chain: B
Molecule details ›
Chain: B
Length: 108 nucleotides
Theoretical weight: 21.13 KDa
Unassigned RNA helices Chain: z
Molecule details ›
Chain: z
Length: 76 nucleotides
Theoretical weight: 14.86 KDa
5' external transcribed spacer Chain: 0
Molecule details ›
Chain: 0
Length: 364 nucleotides
Theoretical weight: 72.8 KDa
18S Ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 1800 nucleotides
Theoretical weight: 579.76 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
U3 snoRNA Chain: 2
Molecule details ›
Chain: 2
Length: 126 nucleotides
Theoretical weight: 37.61 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.1Å
Relevant EMDB volumes: EMD-8473

Quick links

Citations

22 review citations

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

3 mentions without citation

Placeholder factors in ribosome biogenesis: please, pave my way.
Espinar-Marchena et al. (2017)
2 more