› 8cg8

Electron Microscopy
2.57Å resolution

Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

Released:
DOI: 10.2210/pdb8cg8/pdb
PDB entry 8cg8 coloured by chain, front view.
PDB entry 8cg8 coloured by chain, side view.
PDB entry 8cg8 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
mRNA reading frame maintenance during eukaryotic ribosome translocation.
Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G
Nature (2023)
PMID: 38030725
Related structures: EMD-16634

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 84-mer (preferred)
PDBe Complex ID:
PDB-CPX-244709 (preferred)
Entry contents:
77 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (84 distinct):
Small ribosomal subunit protein eS24A Chain: 0
Molecule details ›
Chain: 0
Length: 135 amino acids
Theoretical weight: 15.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX31 (Residues: 1-135; Coverage: 100%)
Gene names: RPS24A, RPS24EA, YER074W
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS25A Chain: 1
Molecule details ›
Chain: 1
Length: 108 amino acids
Theoretical weight: 12.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E792 (Residues: 1-108; Coverage: 100%)
Gene names: RPS25A, RPS31A, YGR027C
Sequence domains: S25 ribosomal protein
40S ribosomal protein S26 Chain: 2
Molecule details ›
Chain: 2
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein eS27A Chain: 3
Molecule details ›
Chain: 3
Length: 82 amino acids
Theoretical weight: 8.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P35997 (Residues: 1-82; Coverage: 100%)
Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS28A Chain: 4
Molecule details ›
Chain: 4
Length: 67 amino acids
Theoretical weight: 7.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E7X9 (Residues: 1-67; Coverage: 100%)
Gene names: O3600, RPS28A, RPS33, RPS33A, YOR167C
Sequence domains: Ribosomal protein S28e
HLJ1_G0030400.mRNA.1.CDS.1 Chain: 5
Molecule details ›
Chain: 5
Length: 56 amino acids
Theoretical weight: 6.68 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein eS30A Chain: 6
Molecule details ›
Chain: 6
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX33 (Residues: 1-63; Coverage: 100%)
Gene names: L8003.23, RPS30A, YLR287BC, YLR287C-A
Sequence domains: Ribosomal protein S30
Small ribosomal subunit protein RACK1 Chain: 7
Molecule details ›
Chain: 7
Length: 319 amino acids
Theoretical weight: 34.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38011 (Residues: 1-319; Coverage: 100%)
Gene names: ASC1, CPC2, YM9718.15C, YMR116C
Sequence domains: WD domain, G-beta repeat
Ubiquitin-40S ribosomal protein S31 Chain: 8
Molecule details ›
Chain: 8
Length: 152 amino acids
Theoretical weight: 17.25 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein uL13A Chain: A
Molecule details ›
Chain: A
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26784 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Elongation factor 2 Chain: Aa
Molecule details ›
Chain: Aa
Length: 842 amino acids
Theoretical weight: 93.55 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein uL22A Chain: B
Molecule details ›
Chain: B
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05740 (Residues: 1-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: C
Molecule details ›
Chain: C
Length: 186 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX49 (Residues: 1-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19A Chain: D
Molecule details ›
Chain: D
Length: 189 amino acids
Theoretical weight: 21.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX82 (Residues: 1-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein uL10 Chain: DD
Molecule details ›
Chain: DD
Length: 312 amino acids
Theoretical weight: 33.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05317 (Residues: 1-312; Coverage: 100%)
Gene names: L10E, L8300.8, RPA0, RPL10E, RPLA0, RPP0, YLR340W
Sequence domains:
Large ribosomal subunit protein eL20A Chain: E
Molecule details ›
Chain: E
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein uL2A Chain: EE
Molecule details ›
Chain: EE
Length: 254 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX45 (Residues: 1-254; Coverage: 100%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
Large ribosomal subunit protein uL11A Chain: Ee
Molecule details ›
Chain: Ee
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX53 (Residues: 1-165; Coverage: 100%)
Gene names: RPL12A, RPL15B, YEL054C
Sequence domains:
Large ribosomal subunit protein eL21A Chain: F
Molecule details ›
Chain: F
Length: 160 amino acids
Theoretical weight: 18.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02753 (Residues: 1-160; Coverage: 100%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein uL3 Chain: FF
Molecule details ›
Chain: FF
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14126 (Residues: 1-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein eL22A Chain: G
Molecule details ›
Chain: G
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05749 (Residues: 1-121; Coverage: 100%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL4A Chain: GG
Molecule details ›
Chain: GG
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10664 (Residues: 1-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
Large ribosomal subunit protein uL14A Chain: H
Molecule details ›
Chain: H
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX41 (Residues: 1-137; Coverage: 100%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL18 Chain: HH
Molecule details ›
Chain: HH
Length: 297 amino acids
Theoretical weight: 33.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26321 (Residues: 1-297; Coverage: 100%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
Large ribosomal subunit protein eL24A Chain: I
Molecule details ›
Chain: I
Length: 155 amino acids
Theoretical weight: 17.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04449 (Residues: 1-155; Coverage: 100%)
Gene names: RP29, RPL24A, RPL30A, YGL031C
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein eL6A Chain: II
Molecule details ›
Chain: II
Length: 176 amino acids
Theoretical weight: 20 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02326 (Residues: 1-176; Coverage: 100%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL23 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04456 (Residues: 1-142; Coverage: 100%)
Gene names: RPL25, YOL127W
Sequence domains:
Large ribosomal subunit protein uL30A Chain: JJ
Molecule details ›
Chain: JJ
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05737 (Residues: 1-244; Coverage: 100%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein uL24A Chain: K
Molecule details ›
Chain: K
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05743 (Residues: 1-127; Coverage: 100%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Large ribosomal subunit protein eL8A Chain: KK
Molecule details ›
Chain: KK
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17076 (Residues: 1-256; Coverage: 100%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL27A Chain: L
Molecule details ›
Chain: L
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H6 (Residues: 1-136; Coverage: 100%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
RPL9A isoform 1 Chain: LL
Molecule details ›
Chain: LL
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein uL15 Chain: M
Molecule details ›
Chain: M
Length: 149 amino acids
Theoretical weight: 16.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02406 (Residues: 1-149; Coverage: 100%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: MM
Molecule details ›
Chain: MM
Length: 221 amino acids
Theoretical weight: 25.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41805 (Residues: 1-221; Coverage: 100%)
Gene names: GRC5, QSR1, RPL10, YLR075W
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein eL29 Chain: N
Molecule details ›
Chain: N
Length: 59 amino acids
Theoretical weight: 6.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05747 (Residues: 1-59; Coverage: 100%)
Gene names: RPL29, YFR032BW, YFR032C-A, YL43
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein uL5A Chain: NN
Molecule details ›
Chain: NN
Length: 174 amino acids
Theoretical weight: 19.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0W9 (Residues: 1-174; Coverage: 100%)
Gene names: P8283.14, RP39A, RPL11A, RPL16A, YPR102C
Sequence domains:
Large ribosomal subunit protein eL30 Chain: O
Molecule details ›
Chain: O
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14120 (Residues: 1-105; Coverage: 100%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL13A Chain: OO
Molecule details ›
Chain: OO
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12690 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL31A Chain: P
Molecule details ›
Chain: P
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H8 (Residues: 1-113; Coverage: 100%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL14A Chain: PP
Molecule details ›
Chain: PP
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36105 (Residues: 1-138; Coverage: 100%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Polypeptide Chain: Pp
Molecule details ›
Chain: Pp
Length: 2 amino acids
Theoretical weight: 296 Da
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein eL32 Chain: Q
Molecule details ›
Chain: Q
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL15A Chain: QQ
Molecule details ›
Chain: QQ
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05748 (Residues: 1-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein eL33A Chain: R
Molecule details ›
Chain: R
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05744 (Residues: 1-107; Coverage: 100%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34A Chain: S
Molecule details ›
Chain: S
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29A Chain: T
Molecule details ›
Chain: T
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX84 (Residues: 1-120; Coverage: 100%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36A Chain: U
Molecule details ›
Chain: U
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05745 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37A Chain: V
Molecule details ›
Chain: V
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chain: W
Molecule details ›
Chain: W
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: X
Molecule details ›
Chain: X
Length: 51 amino acids
Theoretical weight: 6.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04650 (Residues: 1-51; Coverage: 100%)
Gene names: J0360, RPL39, RPL46, SPB2, YJL189W
Sequence domains: Ribosomal L39 protein
Ubiquitin-ribosomal protein eL40A fusion protein Chain: Y
Molecule details ›
Chain: Y
Length: 128 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CH08 (Residues: 1-128; Coverage: 100%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains:
60S ribosomal protein L41 Chain: Z
Molecule details ›
Chain: Z
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Saccharomyces cerevisiae
Large ribosomal subunit protein eL42A Chain: a
Molecule details ›
Chain: a
Length: 106 amino acids
Theoretical weight: 12.25 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX27 (Residues: 1-106; Coverage: 100%)
Gene names: N1722, RPL41A, RPL42A, SCL41A, YNL162W
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43A Chain: b
Molecule details ›
Chain: b
Length: 92 amino acids
Theoretical weight: 10.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX25 (Residues: 1-92; Coverage: 100%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
Small ribosomal subunit protein uS2A Chain: d
Molecule details ›
Chain: d
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: e
Molecule details ›
Chain: e
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: f
Molecule details ›
Chain: f
Length: 254 amino acids
Theoretical weight: 27.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25443 (Residues: 1-254; Coverage: 100%)
Gene names: G2893, RPS2, RPS4, SUP38, SUP44, YGL123W
Sequence domains:
RPS3 isoform 1 Chain: g
Molecule details ›
Chain: g
Length: 240 amino acids
Theoretical weight: 26.54 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein eS4A Chain: h
Molecule details ›
Chain: h
Length: 261 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX35 (Residues: 1-261; Coverage: 100%)
Gene names: J2186, RPS4A, RPS7B, YJR145C
Sequence domains:
Small ribosomal subunit protein uS7 Chain: i
Molecule details ›
Chain: i
Length: 225 amino acids
Theoretical weight: 25.07 KDa
Source organism: Saccharomyces cerevisiae
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: j
Molecule details ›
Chain: j
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX37 (Residues: 1-236; Coverage: 100%)
Gene names: LPG18C, RPS101, RPS10B, RPS6A, YPL090C
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS7A Chain: k
Molecule details ›
Chain: k
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26786 (Residues: 1-190; Coverage: 100%)
Gene names: RPS30, RPS7A, YOR096W, YOR3177W
Sequence domains: Ribosomal protein S7e
Small ribosomal subunit protein eS8B Chain: l
Molecule details ›
Chain: l
Length: 200 amino acids
Theoretical weight: 22.54 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX40 (Residues: 1-200; Coverage: 100%)
Gene names: RPS14B, RPS8B, YER102W
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4A Chain: m
Molecule details ›
Chain: m
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13516 (Residues: 1-197; Coverage: 100%)
Gene names: RPS13A, RPS9A, YPL081W, YS11A
Sequence domains:
Small ribosomal subunit protein eS10A Chain: n
Molecule details ›
Chain: n
Length: 105 amino acids
Theoretical weight: 12.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08745 (Residues: 1-105; Coverage: 100%)
Gene names: RPS10A, YOR293W
Sequence domains: Plectin/S10 domain
Small ribosomal subunit protein uS17A Chain: o
Molecule details ›
Chain: o
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX47 (Residues: 1-156; Coverage: 100%)
Gene names: RPS11A, RPS18A, YD9813.03, YDR025W
Sequence domains:
Small ribosomal subunit protein uS15 Chain: p
Molecule details ›
Chain: p
Length: 151 amino acids
Theoretical weight: 17.06 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05756 (Residues: 1-151; Coverage: 100%)
Gene names: D4252, RPS13, RPS13C, YD9609.18, YDR064W
Sequence domains:
Small ribosomal subunit protein uS11A Chain: q
Molecule details ›
Chain: q
Length: 137 amino acids
Theoretical weight: 14.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P06367 (Residues: 1-137; Coverage: 100%)
Gene names: CRY1, RPL59, RPS14A, YCR031C, YCR31C
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS19 Chain: r
Molecule details ›
Chain: r
Length: 142 amino acids
Theoretical weight: 16.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01855 (Residues: 1-142; Coverage: 100%)
Gene names: RPS15, RPS21, YOL040C
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS9A Chain: s
Molecule details ›
Chain: s
Length: 143 amino acids
Theoretical weight: 15.88 KDa
Source organism: Saccharomyces cerevisiae
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 eS17A Chain: t
Molecule details ›
Chain: t
Length: 136 amino acids
Theoretical weight: 15.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02407 (Residues: 1-136; Coverage: 100%)
Gene names: RP51A, RPS17A, YML024W
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS13A Chain: u
Molecule details ›
Chain: u
Length: 146 amino acids
Theoretical weight: 17.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX55 (Residues: 1-146; Coverage: 100%)
Gene names: D9461.35, RPS18A, YDR450W
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein eS19A Chain: v
Molecule details ›
Chain: v
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07280 (Residues: 1-144; Coverage: 100%)
Gene names: RP55A, RPS16AA, RPS19A, YOL121C
Sequence domains: Ribosomal protein S19e
40S ribosomal protein S20 Chain: w
Molecule details ›
Chain: w
Length: 121 amino acids
Theoretical weight: 13.93 KDa
Source organism: Saccharomyces cerevisiae
Small ribosomal subunit protein eS21A Chain: x
Molecule details ›
Chain: x
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0V8 (Residues: 1-87; Coverage: 100%)
Gene names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Sequence domains: Ribosomal protein S21e
Small ribosomal subunit protein uS8A Chain: y
Molecule details ›
Chain: y
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C0W1 (Residues: 1-130; Coverage: 100%)
Gene names: J0355, RPS22A, RPS24, RPS24A, YJL190C
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS12A Chain: z
Molecule details ›
Chain: z
Length: 145 amino acids
Theoretical weight: 16.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX29 (Residues: 1-145; Coverage: 100%)
Gene names: G6178, RPS23A, RPS28A, YGR118W
Sequence domains: Ribosomal protein S12/S23
25S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 3396 nucleotides
Theoretical weight: 1098.08 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA
Transfer RNA Phe Chain: Bb
Molecule details ›
Chain: Bb
Length: 76 nucleotides
Theoretical weight: 24.74 KDa
Sequence domains: tRNA
5.8S ribosomal RNA Chain: CC
Molecule details ›
Chain: CC
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
Transfer RNA fMet Chain: Cc
Molecule details ›
Chain: Cc
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
Messenger RNA Chain: Dd
Molecule details ›
Chain: Dd
Length: 39 nucleotides
Theoretical weight: 12.74 KDa
18S Ribosomal RNA Chain: c
Molecule details ›
Chain: c
Length: 1800 nucleotides
Theoretical weight: 580.28 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

6 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 241 x MG
Ligand SPD 8 x SPD
Ligand K 19 x K
Ligand GTP 1 x GTP
Ligand SO1 1 x SO1
11 modified residues:
Ligand 1MA 2 x 1MA
Ligand A2M 20 x A2M
Ligand OMC 10 x OMC
Ligand OMG 15 x OMG
Ligand OMU 10 x OMU
Ligand 5MC 2 x 5MC
Ligand UR3 1 x UR3
Ligand DDE 1 x DDE
Ligand YYG 1 x YYG
Ligand G7M 1 x G7M
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.57Å
Relevant EMDB volumes: EMD-16634

Quick links

Citations

1 review citation

Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation.
Yared et al. (2024)