4V8P

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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.

(2011) Science 334: 941

  • DOI: 10.1126/science.1211204
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein synthesis in all organisms is catalyzed by ribosomes. In comparison to their prokaryotic counterparts, eukaryotic ribosomes are considerably larger and are subject to more complex regulation. The large ribosomal subunit (60S) catalyzes peptid ...

    Protein synthesis in all organisms is catalyzed by ribosomes. In comparison to their prokaryotic counterparts, eukaryotic ribosomes are considerably larger and are subject to more complex regulation. The large ribosomal subunit (60S) catalyzes peptide bond formation and contains the nascent polypeptide exit tunnel. We present the structure of the 60S ribosomal subunit from Tetrahymena thermophila in complex with eukaryotic initiation factor 6 (eIF6), cocrystallized with the antibiotic cycloheximide (a eukaryotic-specific inhibitor of protein synthesis), at a resolution of 3.5 angstroms. The structure illustrates the complex functional architecture of the eukaryotic 60S subunit, which comprises an intricate network of interactions between eukaryotic-specific ribosomal protein features and RNA expansion segments. It reveals the roles of eukaryotic ribosomal protein elements in the stabilization of the active site and the extent of eukaryotic-specific differences in other functional regions of the subunit. Furthermore, it elucidates the molecular basis of the interaction with eIF6 and provides a structural framework for further studies of ribosome-associated diseases and the role of the 60S subunit in the initiation of protein synthesis.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L37AA, DA, FA, HA94Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ24 (Tetrahymena thermophila (strain SB210))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RPL39AB, DB, FB, HB52Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ61 (Tetrahymena thermophila (strain SB210))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36AAC, DC, FC, HC109Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22X38 (Tetrahymena thermophila (strain SB210))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RPL6AE, DE, FE, HE191Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ56 (Tetrahymena thermophila (strain SB210))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RPL14AF, DF, FF, HF126Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q24C27 (Tetrahymena thermophila (strain SB210))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RPL30AG, DG, FG, HG104Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RPL35AAH, DH, FH, HH113Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ22 (Tetrahymena thermophila (strain SB210))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEINAJ, DJ, FJ, HJ248Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q245F2 (Tetrahymena thermophila (strain SB210))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-60S RIBOSOMAL PROTEIN L40AK, DK, FK, HK129Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ25 (Tetrahymena thermophila (strain SB210))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPL34AL, DL, FL, HL123Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L22AM, DM, FM, HM118Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23BV5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RPL27AN, DN, FN, HN144Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL27
Find proteins for P0DJ19 (Tetrahymena thermophila)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RPL28AO, DO, FO, HO134Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL28
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RPL38AP, DP, FP, HP89Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22SV3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36AQ, DQ, FQ, HQ104Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q24F59 (Tetrahymena thermophila (strain SB210))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RPL29AT, DT, FT, HT66Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL29
Find proteins for P0DJ21 (Tetrahymena thermophila)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RPL13AU, DU, FU, HU206Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ58 (Tetrahymena thermophila (strain SB210))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RPL18AAX, DX, FX, HX189Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL18ARPL20
Find proteins for P0DJ18 (Tetrahymena thermophila)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RPL8BA, CA, EA, GA264Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ52 (Tetrahymena thermophila (strain SB210))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L3BB, CB, EB, GB391Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL3
Find proteins for O96774 (Tetrahymena thermophila)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RPL4BC, CC, EC, GC410Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ55 (Tetrahymena thermophila (strain SB210))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L11BD, CD, ED, GD172Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL11
Find proteins for P24119 (Tetrahymena thermophila)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L9BE, CE, EE, GE188Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22AX5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RPL7ABF, CF, EF, GF255Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL7ARPL8
Find proteins for P0DJ14 (Tetrahymena thermophila)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RPLP0BG, CG, EG, GG123Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L10BH, CH, EH, GH215Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q235M8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L13ABI, CI, EI, GI198Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ15 (Tetrahymena thermophila (strain SB210))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RPL23BJ, CJ, EJ, GJ141Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ53 (Tetrahymena thermophila (strain SB210))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L27ABK, CK, EK, GK149Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL27ARPL28
Find proteins for Q00454 (Tetrahymena thermophila)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15BL, CL, EL, GL204Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22A30 (Tetrahymena thermophila (strain SB210))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L5BM, CM, EM, GM301Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q231U7 (Tetrahymena thermophila (strain SB210))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RPL18BN, CN, EN, GN181Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL18
Find proteins for P0DJ17 (Tetrahymena thermophila)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
RPL19BO, EO, GO185Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L21BP, CP, EP, GP157Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23TC8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RPL17BQ, CQ, EQ, GQ183Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ16 (Tetrahymena thermophila (strain SB210))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
RPL23ABR, CR, ER, GR150Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ57 (Tetrahymena thermophila (strain SB210))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
RPL26BS, CS, ES, GS135Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23F79 (Tetrahymena thermophila (strain SB210))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
RPL24BT, CT, ET, GT158Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ54 (Tetrahymena thermophila (strain SB210))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
RPL35BU, CU, EU, GU124Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ51 (Tetrahymena thermophila (strain SB210))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L7BV, CV, EV, GV239Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL7
Find proteins for P0DJ13 (Tetrahymena thermophila)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L31BW, CW, EW, GW111Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22DH9 (Tetrahymena thermophila (strain SB210))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L32BX, CX, EX, GX134Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q236T0 (Tetrahymena thermophila (strain SB210))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
RPL37ABY, CY, EY, GY103Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23G98 (Tetrahymena thermophila (strain SB210))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
RPL19CO185Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
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Entity ID: 1
MoleculeChainsLengthOrganism
26S RRNAA1, D1, F1, H13354Tetrahymena thermophila

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Entity ID: 20
MoleculeChainsLengthOrganism
5.8S RRNAB2, C2, E2, G2154Tetrahymena thermophila

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Entity ID: 21
MoleculeChainsLengthOrganism
5S RRNAB3, C3, E3, G3120Tetrahymena thermophila
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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AA, AC, AK, AL, BY, CY, DA, DC, DK, DL, EY, FA, FC, FK, FL, GY, HA, HC, HK, HL
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A1, AA, AK, B2, B3, BJ, BL, BN, BP, BQ, BW, C2, C3, CD, CJ, CL, CN, CQ, CW, CY, D1, DA, DJ, DK, DQ, E2, E3, EJ, EL, EN, EQ, EW, F1, FA, FK, FT, G2, G3, GA, GJ, GL, GN, GO, GP, GQ, GW, H1, HT
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 320.19α = 90
b = 289.25β = 91.22
c = 535.04γ = 90
Software Package:
Software NamePurpose
PHASERmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other