6zqa

Electron Microscopy
4.4Å resolution

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala)

Released:
Related structures: EMD-11357

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:

Structure analysis Details

Assembly composition:
hetero 60-mer (preferred)
PDBe Complex ID:
PDB-CPX-126870 (preferred)
Entry contents:
54 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (57 distinct):
Periodic tryptophan protein 2 Chain: UA
Molecule details ›
Chain: UA
Length: 923 amino acids
Theoretical weight: 104.1 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25635 (Residues: 1-923; Coverage: 100%)
Gene names: PWP2, UTP1, YCR057C, YCR55C/YCR57C/YCR58C
Sequence domains:
Nucleolar complex protein 14 Chain: UB
Molecule details ›
Chain: UB
Length: 810 amino acids
Theoretical weight: 94.46 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q99207 (Residues: 1-810; Coverage: 100%)
Gene names: D1566, NOP14, UTP2, YDL148C
Sequence domains: Nop14-like family
Something about silencing protein 10 Chain: UC
U3 small nucleolar RNA-associated protein 4 Chain: UD
U3 small nucleolar RNA-associated protein 5 Chain: UE
U3 small nucleolar RNA-associated protein 6 Chain: UF
U3 small nucleolar RNA-associated protein 7 Chain: UG
U3 small nucleolar RNA-associated protein 8 Chain: UH
U3 small nucleolar RNA-associated protein 9 Chain: UI
U3 small nucleolar RNA-associated protein 10 Chain: UJ
U3 small nucleolar RNA-associated protein 11 Chain: UK
U3 small nucleolar RNA-associated protein 12 Chain: UL
U3 small nucleolar RNA-associated protein 13 Chain: UM
U3 small nucleolar RNA-associated protein 14 Chain: UN
U3 small nucleolar RNA-associated protein 15 Chain: UO
U3 small nucleolar RNA-associated protein 16 Chain: UP
NET1-associated nuclear protein 1 Chain: UQ
U3 small nucleolar RNA-associated protein 18 Chain: UR
Nucleolar complex protein 4 Chain: US
U3 small nucleolar RNA-associated protein 21 Chain: UU
U3 small nucleolar RNA-associated protein 22 Chain: UV
rRNA-processing protein FCF1 Chain: UX
Ribosome biogenesis protein UTP30 Chain: UZ
rRNA 2'-O-methyltransferase fibrillarin Chains: CA, CB
Nucleolar protein 56 Chain: CD
Nucleolar protein 58 Chain: CE
13 kDa ribonucleoprotein-associated protein Chains: CF, CG
Ribosomal RNA-processing protein 9 Chain: CH
U3 small nucleolar ribonucleoprotein protein IMP3 Chain: CI
U3 small nucleolar ribonucleoprotein protein IMP4 Chain: CJ
U3 small nucleolar RNA-associated protein MPP10 Chain: CK
Ribosome biogenesis protein BMS1 Chain: CL
RNA 3'-terminal phosphate cyclase-like protein Chain: CM
Ribosomal RNA-processing protein 7 Chain: CN
Ribosomal RNA small subunit methyltransferase NEP1 Chains: JF, JG
Essential nuclear protein 1 Chain: JH
Pre-rRNA-processing protein PNO1 Chain: JJ
rRNA-processing protein FCF2 Chain: JM
Protein FAF1 Chain: JN
KRR1 small subunit processome component Chain: JO
Protein SOF1 Chain: JP
Regulator of rDNA transcription protein 14 Chain: JQ
Small ribosomal subunit protein eS1A Chain: DA
Small ribosomal subunit protein uS7 Chain: DF
Small ribosomal subunit protein eS7A Chain: DH
Small ribosomal subunit protein uS4A Chain: DJ
Small ribosomal subunit protein uS15 Chain: DN
Small ribosomal subunit protein uS11A Chain: DO
Small ribosomal subunit protein uS9A Chain: DQ
Small ribosomal subunit protein uS13A Chain: DS
Small ribosomal subunit protein uS8A Chain: DW
Small ribosomal subunit protein uS12A Chain: DX
Small ribosomal subunit protein eS27A Chain: Db
Small ribosomal subunit protein eS28A Chain: Dc
5ETS RNA Chain: D2
18S Ribosomal RNA Chain: D3
U3 snoRNA Chain: D4

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-11357