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 L37
AA, DA, FA, HA
94Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ24 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  P0DJ24

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36A
AC, DC, FC, HC
109Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22X38 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22X38

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RPL6
AE, DE, FE, HE
191Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ56 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  P0DJ56

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RPL14
AF, DF, FF, HF
126Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q24C27 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q24C27

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RPL30
AG, DG, FG, HG
104Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ59 (Tetrahymena thermophila (strain SB210))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RPL35A
AH, DH, FH, HH
113Tetrahymena 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 PROTEIN
AJ, DJ, FJ, HJ
248Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q245F2 (Tetrahymena thermophila (strain SB210))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPL34
AL, DL, FL, HL
123Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ23 (Tetrahymena thermophila (strain SB210))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L22
AM, DM, FM, HM
118Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23BV5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RPL27
AN, DN, FN, HN
144Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL27
Find proteins for P0DJ19 (Tetrahymena thermophila)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RPL28
AO, DO, FO, HO
134Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL28
Find proteins for P0DJ20 (Tetrahymena thermophila)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RPL38
AP, DP, FP, HP
89Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22SV3 (Tetrahymena thermophila (strain SB210))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36
AQ, DQ, FQ, HQ
104Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q24F59 (Tetrahymena thermophila (strain SB210))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RPL29
AT, DT, FT, HT
66Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL29
Find proteins for P0DJ21 (Tetrahymena thermophila)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RPL13
AU, DU, FU, HU
206Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ58 (Tetrahymena thermophila (strain SB210))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RPL18A
AX, DX, FX, HX
189Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL18ARPL20
Find proteins for P0DJ18 (Tetrahymena thermophila)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RPL8
BA, CA, EA, GA
264Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ52 (Tetrahymena thermophila (strain SB210))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L3
BB, CB, EB, GB
391Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL3
Find proteins for O96774 (Tetrahymena thermophila)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RPL4
BC, CC, EC, GC
410Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ55 (Tetrahymena thermophila (strain SB210))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L11
BD, CD, ED, GD
172Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL11
Find proteins for P24119 (Tetrahymena thermophila)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L9
BE, CE, EE, GE
188Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22AX5 (Tetrahymena thermophila (strain SB210))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RPL7A
BF, CF, EF, GF
255Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL7ARPL8
Find proteins for P0DJ14 (Tetrahymena thermophila)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RPLP0
BG, CG, EG, GG
123Tetrahymena thermophilaMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L10
BH, CH, EH, GH
215Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q235M8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RPL23
BJ, CJ, EJ, GJ
141Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ53 (Tetrahymena thermophila (strain SB210))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L27A
BK, CK, EK, GK
149Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL27ARPL28
Find proteins for Q00454 (Tetrahymena thermophila)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15
BL, CL, EL, GL
204Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22A30 (Tetrahymena thermophila (strain SB210))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L5
BM, CM, EM, GM
301Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q231U7 (Tetrahymena thermophila (strain SB210))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RPL18
BN, CN, EN, GN
181Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL18
Find proteins for P0DJ17 (Tetrahymena thermophila)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L21
BP, CP, EP, GP
157Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23TC8 (Tetrahymena thermophila (strain SB210))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RPL17
BQ, CQ, EQ, GQ
183Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ16 (Tetrahymena thermophila (strain SB210))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
RPL23A
BR, CR, ER, GR
150Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ57 (Tetrahymena thermophila (strain SB210))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
RPL26
BS, CS, ES, GS
135Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23F79 (Tetrahymena thermophila (strain SB210))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
RPL24
BT, CT, ET, GT
158Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ54 (Tetrahymena thermophila (strain SB210))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
RPL35
BU, CU, EU, GU
124Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ51 (Tetrahymena thermophila (strain SB210))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L7
BV, CV, EV, GV
239Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL7
Find proteins for P0DJ13 (Tetrahymena thermophila)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L32
BX, CX, EX, GX
134Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q236T0 (Tetrahymena thermophila (strain SB210))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
RPL37A
BY, CY, EY, GY
103Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q23G98 (Tetrahymena thermophila (strain SB210))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
RPL19
CO
185Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-60S RIBOSOMAL PROTEIN L40
AK, DK, FK, HK
129Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ25 (Tetrahymena thermophila (strain SB210))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RPL39
AB, DB, FB, HB
52Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ61 (Tetrahymena thermophila (strain SB210))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L13A
BI, CI, EI, GI
198Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ15 (Tetrahymena thermophila (strain SB210))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
RPL19
BO, EO, GO
185Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L31
BW, CW, EW, GW
111Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q22DH9 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22DH9

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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

Download CCD File 
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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