› 4v8p

X-ray diffraction
3.52Å resolution

T.thermophila 60S ribosomal subunit in complex with initiation factor 6.

Released:
DOI: 10.2210/pdb4v8p/pdb
PDB entry 4v8p coloured by chain, front view.
PDB entry 4v8p coloured by chain, side view.
PDB entry 4v8p coloured by chain, top view.
Source organism: Tetrahymena thermophila
Primary publication:
Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6.
Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N
Science 334 941-8 (2011)
PMID: 22052974

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-132159 (preferred)
Entry contents:
44 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (47 distinct):
Large ribosomal subunit protein eL37 Chains: AA, DA, FA, HA
Molecule details ›
Chains: AA, DA, FA, HA
Length: 94 amino acids
Theoretical weight: 10.7 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ24 (Residues: 1-94; Coverage: 100%)
Gene names: RPL37, TTHERM_01068180
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL39 Chains: AB, DB, FB, HB
Molecule details ›
Chains: AB, DB, FB, HB
Length: 52 amino acids
Theoretical weight: 6.61 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ61 (Residues: 1-52; Coverage: 100%)
Gene names: RPL39, TTHERM_00526400A
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL42 Chains: AC, DC, FC, HC
Molecule details ›
Chains: AC, DC, FC, HC
Length: 109 amino acids
Theoretical weight: 12.79 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22X38 (Residues: 1-109; Coverage: 100%)
Gene names: RPL36A, RPL42, RPL44, TTHERM_00633150
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL6 Chains: AE, DE, FE, HE
Molecule details ›
Chains: AE, DE, FE, HE
Length: 191 amino acids
Theoretical weight: 21.78 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ56 (Residues: 1-191; Coverage: 100%)
Gene names: RPL6, TTHERM_00136120A
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein eL14 Chains: AF, DF, FF, HF
Molecule details ›
Chains: AF, DF, FF, HF
Length: 126 amino acids
Theoretical weight: 14.63 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q24C27 (Residues: 1-126; Coverage: 100%)
Gene names: RPL14, TTHERM_00697490A
Sequence domains:
Large ribosomal subunit protein eL30 Chains: AG, DG, FG, HG
Molecule details ›
Chains: AG, DG, FG, HG
Length: 104 amino acids
Theoretical weight: 11.37 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ59 (Residues: 1-104; Coverage: 100%)
Gene names: RPL30, TTHERM_00446280A
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL33 Chains: AH, DH, FH, HH
Molecule details ›
Chains: AH, DH, FH, HH
Length: 113 amino acids
Theoretical weight: 12.65 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ22 (Residues: 1-113; Coverage: 100%)
Gene names: RL33A, RPL35A, TTHERM_00992730
Sequence domains: Ribosomal protein L35Ae
Eukaryotic translation initiation factor 6 Chains: AJ, DJ, FJ, HJ
Molecule details ›
Chains: AJ, DJ, FJ, HJ
Length: 248 amino acids
Theoretical weight: 27.19 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q245F2 (Residues: 1-245; Coverage: 100%)
Gene names: EIF6, TTHERM_00732590
Sequence domains: eIF-6 family
Ubiquitin-ribosomal protein eL40 fusion protein Chains: AK, DK, FK, HK
Molecule details ›
Chains: AK, DK, FK, HK
Length: 129 amino acids
Theoretical weight: 14.6 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ25 (Residues: 1-129; Coverage: 100%)
Gene name: RPL40
Sequence domains:
Large ribosomal subunit protein eL34 Chains: AL, DL, FL, HL
Molecule details ›
Chains: AL, DL, FL, HL
Length: 123 amino acids
Theoretical weight: 14.07 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ23 (Residues: 1-123; Coverage: 100%)
Gene name: RPL34
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein eL22 Chains: AM, DM, FM, HM
Molecule details ›
Chains: AM, DM, FM, HM
Length: 118 amino acids
Theoretical weight: 13.8 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q23BV5 (Residues: 1-118; Coverage: 100%)
Gene names: RPL22, TTHERM_00227270
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein eL27 Chains: AN, DN, FN, HN
Molecule details ›
Chains: AN, DN, FN, HN
Length: 144 amino acids
Theoretical weight: 16.77 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ19 (Residues: 1-144; Coverage: 100%)
Gene name: RPL27
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein eL28 Chains: AO, DO, FO, HO
Molecule details ›
Chains: AO, DO, FO, HO
Length: 134 amino acids
Theoretical weight: 14.7 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ20 (Residues: 1-134; Coverage: 100%)
Gene name: RPL28
Sequence domains: Ribosomal L28e protein family
Large ribosomal subunit protein eL38 Chains: AP, DP, FP, HP
Molecule details ›
Chains: AP, DP, FP, HP
Length: 89 amino acids
Theoretical weight: 10.22 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22SV3 (Residues: 1-89; Coverage: 100%)
Gene names: RPL38, TTHERM_00812780
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL36 Chains: AQ, DQ, FQ, HQ
Molecule details ›
Chains: AQ, DQ, FQ, HQ
Length: 104 amino acids
Theoretical weight: 11.7 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q24F59 (Residues: 1-104; Coverage: 100%)
Gene names: RPL36, TTHERM_01129660
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL29 Chains: AT, DT, FT, HT
Molecule details ›
Chains: AT, DT, FT, HT
Length: 66 amino acids
Theoretical weight: 7.74 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ21 (Residues: 1-66; Coverage: 100%)
Gene name: RPL29
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein eL13 Chains: AU, DU, FU, HU
Molecule details ›
Chains: AU, DU, FU, HU
Length: 206 amino acids
Theoretical weight: 23.39 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ58 (Residues: 1-206; Coverage: 100%)
Gene names: RPL13, TTHERM_00578640A
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL20 Chains: AX, DX, FX, HX
Molecule details ›
Chains: AX, DX, FX, HX
Length: 189 amino acids
Theoretical weight: 22.02 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ18 (Residues: 1-189; Coverage: 100%)
Gene names: RPL18A, RPL20
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein uL2 Chains: BA, CA, EA, GA
Molecule details ›
Chains: BA, CA, EA, GA
Length: 264 amino acids
Theoretical weight: 28.71 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ52 (Residues: 1-264; Coverage: 100%)
Gene names: RPL2, RPL8, TTHERM_00716240
Sequence domains:
Large ribosomal subunit protein uL3 Chains: BB, CB, EB, GB
Molecule details ›
Chains: BB, CB, EB, GB
Length: 391 amino acids
Theoretical weight: 44.35 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: O96774 (Residues: 1-391; Coverage: 100%)
Gene name: RPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: BC, CC, EC, GC
Molecule details ›
Chains: BC, CC, EC, GC
Length: 410 amino acids
Theoretical weight: 45.19 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ55 (Residues: 1-410; Coverage: 100%)
Gene names: RPL4, TTHERM_00333210
Sequence domains:
Large ribosomal subunit protein uL5 Chains: BD, CD, ED, GD
Molecule details ›
Chains: BD, CD, ED, GD
Length: 172 amino acids
Theoretical weight: 19.75 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P24119 (Residues: 1-172; Coverage: 100%)
Gene name: RPL11
Sequence domains:
Large ribosomal subunit protein uL6 Chains: BE, CE, EE, GE
Molecule details ›
Chains: BE, CE, EE, GE
Length: 188 amino acids
Theoretical weight: 21.37 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22AX5 (Residues: 1-188; Coverage: 100%)
Gene names: RPL9, TTHERM_01142730A
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein eL8 Chains: BF, CF, EF, GF
Molecule details ›
Chains: BF, CF, EF, GF
Length: 255 amino acids
Theoretical weight: 29.13 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ14 (Residues: 1-255; Coverage: 100%)
Gene names: RPL7A, RPL8
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
RPLP0 Chains: BG, CG, EG, GG
Molecule details ›
Chains: BG, CG, EG, GG
Length: 123 amino acids
Theoretical weight: 10.49 KDa
Source organism: Tetrahymena thermophila
Large ribosomal subunit protein uL16 Chains: BH, CH, EH, GH
Molecule details ›
Chains: BH, CH, EH, GH
Length: 215 amino acids
Theoretical weight: 24.51 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q235M8 (Residues: 1-215; Coverage: 100%)
Gene names: RPL10, TTHERM_01053000
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL13 Chains: BI, CI, EI, GI
Molecule details ›
Chains: BI, CI, EI, GI
Length: 198 amino acids
Theoretical weight: 22.64 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ15 (Residues: 1-198; Coverage: 100%)
Gene names: RPL13A, RPL16
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: BJ, CJ, EJ, GJ
Molecule details ›
Chains: BJ, CJ, EJ, GJ
Length: 141 amino acids
Theoretical weight: 14.9 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ53 (Residues: 1-141; Coverage: 100%)
Gene names: RPL23, TTHERM_00227270
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: BK, CK, EK, GK
Molecule details ›
Chains: BK, CK, EK, GK
Length: 149 amino acids
Theoretical weight: 16.66 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q00454 (Residues: 1-149; Coverage: 100%)
Gene names: RPL27A, RPL28
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL15 Chains: BL, CL, EL, GL
Molecule details ›
Chains: BL, CL, EL, GL
Length: 204 amino acids
Theoretical weight: 24.13 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22A30 (Residues: 1-204; Coverage: 100%)
Gene names: RPL15, TTHERM_01289110
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL18 Chains: BM, CM, EM, GM
Molecule details ›
Chains: BM, CM, EM, GM
Length: 301 amino acids
Theoretical weight: 34.53 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q231U7 (Residues: 1-301; Coverage: 100%)
Gene names: RPL5, TTHERM_00736480
Sequence domains:
Large ribosomal subunit protein eL18 Chains: BN, CN, EN, GN
Molecule details ›
Chains: BN, CN, EN, GN
Length: 181 amino acids
Theoretical weight: 20.63 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ17 (Residues: 1-181; Coverage: 100%)
Gene name: RPL18
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 Chains: BO, EO, GO
Molecule details ›
Chains: BO, EO, GO
Length: 185 amino acids
Theoretical weight: 21.43 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ60 (Residues: 1-185; Coverage: 100%)
Gene names: RPL19, TTHERM_00444510A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL21 Chains: BP, CP, EP, GP
Molecule details ›
Chains: BP, CP, EP, GP
Length: 157 amino acids
Theoretical weight: 18.16 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q23TC8 (Residues: 1-157; Coverage: 100%)
Gene names: RPL21, TTHERM_00666540
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein uL22 Chains: BQ, CQ, EQ, GQ
Molecule details ›
Chains: BQ, CQ, EQ, GQ
Length: 183 amino acids
Theoretical weight: 20.42 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ16 (Residues: 1-183; Coverage: 100%)
Gene name: RPL17
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: BR, CR, ER, GR
Molecule details ›
Chains: BR, CR, ER, GR
Length: 150 amino acids
Theoretical weight: 16.9 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ57 (Residues: 1-150; Coverage: 100%)
Gene names: RPL23A, RPL25, TTHERM_00134940A
Sequence domains:
Large ribosomal subunit protein uL24 Chains: BS, CS, ES, GS
Molecule details ›
Chains: BS, CS, ES, GS
Length: 135 amino acids
Theoretical weight: 15.42 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q23F79 (Residues: 1-135; Coverage: 100%)
Gene names: RPL26, TTHERM_00382350
Sequence domains:
Large ribosomal subunit protein eL24 Chains: BT, CT, ET, GT
Molecule details ›
Chains: BT, CT, ET, GT
Length: 158 amino acids
Theoretical weight: 18.1 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ54 (Residues: 1-158; Coverage: 100%)
Gene names: RPL24, TTHERM_00476640A
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL29 Chains: BU, CU, EU, GU
Molecule details ›
Chains: BU, CU, EU, GU
Length: 124 amino acids
Theoretical weight: 14.23 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ51 (Residues: 1-124; Coverage: 100%)
Gene names: RPL35, TTHERM_00561680A
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: BV, CV, EV, GV
Molecule details ›
Chains: BV, CV, EV, GV
Length: 239 amino acids
Theoretical weight: 27.67 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ13 (Residues: 1-239; Coverage: 100%)
Gene name: RPL7
Sequence domains:
Large ribosomal subunit protein eL31 Chains: BW, CW, EW, GW
Molecule details ›
Chains: BW, CW, EW, GW
Length: 111 amino acids
Theoretical weight: 12.99 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q22DH9 (Residues: 1-111; Coverage: 100%)
Gene names: RPL31, TTHERM_00943010
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chains: BX, CX, EX, GX
Molecule details ›
Chains: BX, CX, EX, GX
Length: 134 amino acids
Theoretical weight: 15.35 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q236T0 (Residues: 1-134; Coverage: 100%)
Gene names: RPL32, TTHERM_00085180
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL43 Chains: BY, CY, EY, GY
Molecule details ›
Chains: BY, CY, EY, GY
Length: 103 amino acids
Theoretical weight: 11.38 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: Q23G98 (Residues: 1-103; Coverage: 100%)
Gene names: RPL37A, RPL43, TTHERM_00075670
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL19 Chain: CO
Molecule details ›
Chain: CO
Length: 185 amino acids
Theoretical weight: 20.39 KDa
Source organism: Tetrahymena thermophila
UniProt:
  • Canonical: P0DJ60 (Residues: 1-147; Coverage: 80%)
Gene names: RPL19, TTHERM_00444510A
Sequence domains: Ribosomal protein L19e
26S RRNA Chains: A1, D1, F1, H1
Molecule details ›
Chains: A1, D1, F1, H1
Length: 3354 nucleotides
Theoretical weight: 1084.31 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chains: B2, C2, E2, G2
Molecule details ›
Chains: B2, C2, E2, G2
Length: 154 nucleotides
Theoretical weight: 49.8 KDa
Sequence domains: 5.8S ribosomal RNA
5S ribosomal RNA Chains: B3, C3, E3, G3
Molecule details ›
Chains: B3, C3, E3, G3
Length: 120 nucleotides
Theoretical weight: 38.74 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 865 x MG
Ligand ZN 20 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 320.19Å b: 289.25Å c: 535.04Å
α: 90° β: 91.22° γ: 90°
R-values:
R R work R free
0.216 0.216 0.244

Quick links

Citations

69 review citations

Ribosome biogenesis in the yeast Saccharomyces cerevisiae.
Woolford et al. (2013)
68 more

4 mentions without citation

Mechanistic insight into eukaryotic 60S ribosomal subunit biogenesis by cryo-electron microscopy.
Greber BJ. (2016)
3 more