6lqu

Electron Microscopy
3.7Å resolution

Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1)

Released:
Primary publication:
Cryo-EM structure of 90S small ribosomal subunit precursors in transition states.
Science 369 1477-1481 (2020)
PMID: 32943522
Related structures: EMD-0954

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 72-mer (preferred)
PDBe Complex ID:
PDB-CPX-126873 (preferred)
Entry contents:
65 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (68 distinct):
Small ribosomal subunit protein eS4A Chain: SF
Molecule details ›
Chain: SF
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: SG
Molecule details ›
Chain: SG
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 eS6A Chain: SH
Small ribosomal subunit protein eS7A Chain: SI
Small ribosomal subunit protein eS8A Chain: SJ
Small ribosomal subunit protein uS4A Chain: SK
Small ribosomal subunit protein uS17A Chain: SM
Small ribosomal subunit protein eS12 Chain: SN
Small ribosomal subunit protein uS15 Chain: SO
Small ribosomal subunit protein uS11A Chain: SP
Small ribosomal subunit protein uS9A Chain: SR
Small ribosomal subunit protein uS13A Chain: ST
Small ribosomal subunit protein uS8B Chain: SX
Small ribosomal subunit protein uS12A Chain: SY
Small ribosomal subunit protein eS24A Chain: SZ
Small ribosomal subunit protein eS28A Chain: Sd
rRNA 2'-O-methyltransferase fibrillarin Chains: 3B, 3C
Nucleolar protein 56 Chain: 3D
Nucleolar protein 58 Chain: 3E
Ribosomal RNA-processing protein 9 Chain: 3F
13 kDa ribonucleoprotein-associated protein Chains: 3G, 3H
U3 small nucleolar RNA-associated protein 4 Chain: A4
U3 small nucleolar RNA-associated protein 5 Chain: A5
U3 small nucleolar RNA-associated protein 8 Chain: A8
U3 small nucleolar RNA-associated protein 9 Chain: A9
U3 small nucleolar RNA-associated protein 10 Chain: AE
U3 small nucleolar RNA-associated protein 15 Chain: AF
NET1-associated nuclear protein 1 Chain: AG
Periodic tryptophan protein 2 Chain: B1
U3 small nucleolar RNA-associated protein 12 Chain: B2
U3 small nucleolar RNA-associated protein 13 Chain: B3
U3 small nucleolar RNA-associated protein 18 Chain: B8
U3 small nucleolar RNA-associated protein 21 Chain: BE
U3 small nucleolar RNA-associated protein 6 Chain: B6
U3 small nucleolar RNA-associated protein 16 Chain: 5B
U3 small nucleolar RNA-associated protein 7 Chain: 5C
U3 small nucleolar RNA-associated protein 11 Chain: 5D
U3 small nucleolar RNA-associated protein MPP10 Chain: 5E
U3 small nucleolar ribonucleoprotein protein IMP3 Chain: 5F
U3 small nucleolar ribonucleoprotein protein IMP4 Chain: 5G
Something about silencing protein 10 Chain: 5H
Protein SOF1 Chain: 5I
rRNA-processing protein FCF2 Chain: 5J
rRNA-processing protein FCF1 Chain: 5K
Ribosome biogenesis protein ENP2 Chain: RA
U3 small nucleolar ribonucleoprotein protein LCP5 Chain: RB
KRR1 small subunit processome component Chain: RC
rRNA biogenesis protein RRP5 Chain: RD
U3 small nucleolar RNA-associated protein 22 Chain: RE
Ribosomal RNA-processing protein 7 Chain: RF
Ribosomal RNA small subunit methyltransferase NEP1 Chains: RG, RH
Ribosome biogenesis protein UTP30 Chain: RI
Ribosome biogenesis protein BMS1 Chain: RJ
rRNA processing protein RCL1 Chain: RK
RNA cytidine acetyltransferase Chains: RL, RM
Nucleolar complex protein 14 Chain: RN
Nucleolar complex protein 4 Chain: RO
U3 small nucleolar RNA-associated protein 20 Chain: RP
U3 small nucleolar RNA-associated protein 14 Chain: RQ
Essential nuclear protein 1 Chain: RS
Pno1 Chain: RT
Protein FAF1 Chain: RV
Regulator of rDNA transcription protein 14 Chain: RW
Protein BFR2 Chain: RY
Unassigned helices Chain: X1
U3 snoRNA Chain: 3A
5' ETS Chain: 5A
18S pre-rRNA Chain: SA

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.7Å
Relevant EMDB volumes: EMD-0954