› 8k2d

Electron Microscopy
3.2Å resolution

Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A

Released:
DOI: 10.2210/pdb8k2d/pdb
PDB entry 8k2d coloured by chain, front view.
PDB entry 8k2d coloured by chain, side view.
PDB entry 8k2d coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Li X, Wang M, Denk T, Buschauer R, Li Y, Beckmann R, Cheng J
Nat Commun 15 5481 (2024)
PMID: 38942792
Related structures: EMD-36839

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 84-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-271517 (preferred)
Entry contents:
80 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (84 distinct):
Small ribosomal subunit protein uS2A Chain: SA
Molecule details ›
Chain: SA
Length: 252 amino acids
Theoretical weight: 28.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32905 (Residues: 1-252; Coverage: 100%)
Gene names: NAB1, NAB1A, RPS0A, YGR214W, YST1
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS1A Chain: SB
Molecule details ›
Chain: SB
Length: 255 amino acids
Theoretical weight: 28.8 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33442 (Residues: 1-255; Coverage: 100%)
Gene names: L9753.9, PLC1, RPS10A, RPS1A, YLR441C
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS5 Chain: SC
Small ribosomal subunit protein uS3 Chain: SD
Small ribosomal subunit protein eS4A Chain: SE
Small ribosomal subunit protein uS7 Chain: SF
Small ribosomal subunit protein eS6A Chain: SG
Small ribosomal subunit protein eS7A Chain: SH
Small ribosomal subunit protein eS8A Chain: SI
Small ribosomal subunit protein uS4A Chain: SJ
Small ribosomal subunit protein eS10A Chain: SK
Small ribosomal subunit protein uS17A Chain: SL
Small ribosomal subunit protein eS12 Chain: SM
Small ribosomal subunit protein uS15 Chain: SN
Small ribosomal subunit protein uS11A Chain: SO
Small ribosomal subunit protein uS19 Chain: SP
Small ribosomal subunit protein uS9A Chain: SQ
Small ribosomal subunit protein eS17A Chain: SR
Small ribosomal subunit protein uS13A Chain: SS
Small ribosomal subunit protein eS19A Chain: ST
Small ribosomal subunit protein uS10 Chain: SU
Small ribosomal subunit protein eS21A Chain: SV
Small ribosomal subunit protein uS8A Chain: SW
Small ribosomal subunit protein uS12A Chain: SX
Small ribosomal subunit protein eS24A Chain: SY
Small ribosomal subunit protein eS25A Chain: SZ
Small ribosomal subunit protein eS26B Chain: Sa
Small ribosomal subunit protein eS27A Chain: Sb
Small ribosomal subunit protein eS28A Chain: Sc
Small ribosomal subunit protein uS14A Chain: Sd
Small ribosomal subunit protein eS30A Chain: Se
Ubiquitin-ribosomal protein eS31 fusion protein Chain: Sf
Small ribosomal subunit protein RACK1 Chain: Sg
Large ribosomal subunit protein uL2A Chain: LA
Large ribosomal subunit protein uL3 Chain: LB
Large ribosomal subunit protein uL4A Chain: LC
Large ribosomal subunit protein uL18 Chain: LD
Large ribosomal subunit protein eL6A Chain: LE
Large ribosomal subunit protein uL30A Chain: LF
Large ribosomal subunit protein eL8A Chain: LG
Large ribosomal subunit protein uL6A Chain: LH
Large ribosomal subunit protein uL16 Chain: LI
Large ribosomal subunit protein uL5A Chain: LJ
Large ribosomal subunit protein uL11A Chain: LK
Large ribosomal subunit protein eL13A Chain: LL
Large ribosomal subunit protein eL14A Chain: LM
Large ribosomal subunit protein eL15A Chain: LN
Large ribosomal subunit protein uL13A Chain: LO
Large ribosomal subunit protein uL22A Chain: LP
Large ribosomal subunit protein eL18A Chain: LQ
Large ribosomal subunit protein eL19A Chain: LR
Large ribosomal subunit protein eL20A Chain: LS
Large ribosomal subunit protein eL21A Chain: LT
Large ribosomal subunit protein eL22A Chain: LU
Large ribosomal subunit protein uL14A Chain: LV
Large ribosomal subunit protein eL24A Chain: LW
Large ribosomal subunit protein uL23 Chain: LX
Large ribosomal subunit protein uL24A Chain: LY
Large ribosomal subunit protein eL27A Chain: LZ
Large ribosomal subunit protein uL15 Chain: La
Large ribosomal subunit protein eL29 Chain: Lb
Large ribosomal subunit protein eL30 Chain: Lc
Large ribosomal subunit protein eL31A Chain: Ld
Large ribosomal subunit protein eL32 Chain: Le
Large ribosomal subunit protein eL33A Chain: Lf
Large ribosomal subunit protein eL34A Chain: Lg
Large ribosomal subunit protein uL29A Chain: Lh
Large ribosomal subunit protein eL36A Chain: Li
Large ribosomal subunit protein eL37A Chain: Lj
Large ribosomal subunit protein eL38 Chain: Lk
Large ribosomal subunit protein eL39 Chain: Ll
Ubiquitin-ribosomal protein eL40A fusion protein Chain: Lm
Small ribosomal subunit protein eS32A Chain: Ln
Large ribosomal subunit protein eL42A Chain: Lo
Large ribosomal subunit protein eL43A Chain: Lp
Eukaryotic translation initiation factor 5A-1 Chain: CE
Large ribosomal subunit protein uL1A Chain: L1
Large ribosomal subunit protein uL10 Chain: P0
Elongation factor 2 Chain: CD
Suppressor protein STM1 Chain: CS
18S Ribosomal RNA Chain: C2
23S ribosomal RNA Chain: C1
5S ribosomal RNA Chain: C4
5.8S ribosomal RNA Chain: C3

Ligands and Environments

4 bound ligands:
Ligand ZN 9 x ZN
Ligand T1C 6 x T1C
Ligand MG 4 x MG
Ligand GDP 1 x GDP
1 modified residue:
Ligand 5CT 1 x 5CT

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.2Å
Relevant EMDB volumes: EMD-36839

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