7ajt

Electron Microscopy
4.6Å resolution

Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome)

Released:

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + pseudouridine(1191) in yeast 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1191) in yeast 18S rRNA 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 83-mer (preferred)
PDBe Complex ID:
PDB-CPX-292914 (preferred)
Entry contents:
75 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (79 distinct):
rRNA 2'-O-methyltransferase fibrillarin Chains: CA, CB
Molecule details ›
Chains: CA, CB
Length: 327 amino acids
Theoretical weight: 34.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P15646 (Residues: 1-327; Coverage: 100%)
Gene names: D2870, LOT3, NOP1, YDL014W
Sequence domains: Fibrillarin
Small ribosomal subunit protein eS1A Chain: DA
Molecule details ›
Chain: DA
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
RNA cytidine acetyltransferase Chains: JA, JB
Periodic tryptophan protein 2 Chain: UA
Nucleolar complex protein 14 Chain: UB
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 20 Chain: UT
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
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
rRNA processing protein RCL1 Chain: CM
Ribosomal RNA-processing protein 7 Chain: CN
Ribosome biogenesis protein ENP2 Chain: JC
Ribosomal RNA small subunit methyltransferase NEP1 Chains: JF, JG
Essential nuclear protein 1 Chain: JH
rRNA biogenesis protein RRP5 Chain: JI
Pre-rRNA-processing protein PNO1 Chain: JJ
Protein BFR2 Chain: JK
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 eS4A Chain: DE
Small ribosomal subunit protein uS7 Chain: DF
Small ribosomal subunit protein eS6A Chain: DG
Small ribosomal subunit protein eS7A Chain: DH
Small ribosomal subunit protein eS8A Chain: DI
Small ribosomal subunit protein uS4A Chain: DJ
Small ribosomal subunit protein uS17A Chain: DL
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 eS24A Chain: DY
Small ribosomal subunit protein eS27A Chain: Db
Small ribosomal subunit protein eS28A Chain: Dc
Exosome complex component RRP45 Chain: EB
Exosome complex component SKI6 Chain: EC
Exosome complex component RRP43 Chain: ED
Exosome complex component RRP46 Chain: EE
Exosome complex component RRP42 Chain: EF
Exosome complex component MTR3 Chain: EG
Exosome complex component RRP40 Chain: EH
Exosome complex component RRP4 Chain: EI
Exosome complex component CSL4 Chain: EJ
Exosome complex exonuclease DIS3 Chain: EK
ATP-dependent RNA helicase DOB1 Chain: EN
5'ETS RNA Chain: D2
18S Ribosomal RNA Chain: D3
U3 snoRNA Chain: D4
RNA Chain: EA

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 4.6Å
Relevant EMDB volumes: EMD-11807
Expression system: Saccharomyces cerevisiae S288C