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 

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
  • Primary Citation of Related Structures:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L37
AA, DA, FA, HA
94Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL37
Find proteins for P0DJ24 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL37
Go to UniProtKB:  P0DJ24
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RPL39
AB, DB, FB, HB
52Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL39
Find proteins for P0DJ61 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL39
Go to UniProtKB:  P0DJ61
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36A
AC, DC, FC, HC
109Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL36A (RPL42, RPL44)
Find proteins for Q22X38 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL36A
Go to UniProtKB:  Q22X38
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RPL6
AE, DE, FE, HE
191Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL6
Find proteins for P0DJ56 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL6
Go to UniProtKB:  P0DJ56
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RPL14
AF, DF, FF, HF
126Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL14
Find proteins for Q24C27 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL14
Go to UniProtKB:  Q24C27
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RPL30
AG, DG, FG, HG
104Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL30
Find proteins for P0DJ59 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL30
Go to UniProtKB:  P0DJ59
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RPL35A
AH, DH, FH, HH
113Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL35A (RL33A)
Find proteins for P0DJ22 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL35A
Go to UniProtKB:  P0DJ22
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEIN
AJ, DJ, FJ, HJ
248Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: EIF6
Find proteins for Q245F2 (Tetrahymena thermophila (strain SB210))
Go to Gene View: EIF6
Go to UniProtKB:  Q245F2
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-60S RIBOSOMAL PROTEIN L40
AK, DK, FK, HK
129Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL40
Find proteins for P0DJ25 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  P0DJ25
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RPL34
AL, DL, FL, HL
123Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL34
Find proteins for P0DJ23 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL34
Go to UniProtKB:  P0DJ23
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L22
AM, DM, FM, HM
118Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL22
Find proteins for Q23BV5 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL22
Go to UniProtKB:  Q23BV5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RPL27
AN, DN, FN, HN
144Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL27
Find proteins for P0DJ19 (Tetrahymena thermophila)
Go to Gene View: RPL27
Go to UniProtKB:  P0DJ19
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RPL28
AO, DO, FO, HO
134Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL28
Find proteins for P0DJ20 (Tetrahymena thermophila)
Go to Gene View: RPL28
Go to UniProtKB:  P0DJ20
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RPL38
AP, DP, FP, HP
89Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL38
Find proteins for Q22SV3 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL38
Go to UniProtKB:  Q22SV3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36
AQ, DQ, FQ, HQ
104Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL36
Find proteins for Q24F59 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL36
Go to UniProtKB:  Q24F59
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RPL29
AT, DT, FT, HT
66Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL29
Find proteins for P0DJ21 (Tetrahymena thermophila)
Go to Gene View: RPL29
Go to UniProtKB:  P0DJ21
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RPL13
AU, DU, FU, HU
206Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL13
Find proteins for P0DJ58 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL13
Go to UniProtKB:  P0DJ58
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RPL18A
AX, DX, FX, HX
189Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL18A (RPL20)
Find proteins for P0DJ18 (Tetrahymena thermophila)
Go to Gene View: RPL18A
Go to UniProtKB:  P0DJ18
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RPL8
BA, CA, EA, GA
264Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL8 (RPL2)
Find proteins for P0DJ52 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL8
Go to UniProtKB:  P0DJ52
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)
Go to Gene View: RPL3
Go to UniProtKB:  O96774
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RPL4
BC, CC, EC, GC
410Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL4
Find proteins for P0DJ55 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL4
Go to UniProtKB:  P0DJ55
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)
Go to Gene View: RPL11
Go to UniProtKB:  P24119
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L9
BE, CE, EE, GE
188Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL9
Find proteins for Q22AX5 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL9
Go to UniProtKB:  Q22AX5
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RPL7A
BF, CF, EF, GF
255Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL7A (RPL8)
Find proteins for P0DJ14 (Tetrahymena thermophila)
Go to Gene View: RPL7A
Go to UniProtKB:  P0DJ14
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RPLP0
BG, CG, EG, GG
123N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L10
BH, CH, EH, GH
215Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL10
Find proteins for Q235M8 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL10
Go to UniProtKB:  Q235M8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L13A
BI, CI, EI, GI
198Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL13A (RPL16)
Find proteins for P0DJ15 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL13A
Go to UniProtKB:  P0DJ15
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RPL23
BJ, CJ, EJ, GJ
141Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL23
Find proteins for P0DJ53 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL23
Go to UniProtKB:  P0DJ53
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L27A
BK, CK, EK, GK
149Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL27A (RPL28)
Find proteins for Q00454 (Tetrahymena thermophila)
Go to Gene View: RPL27A
Go to UniProtKB:  Q00454
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15
BL, CL, EL, GL
204Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL15
Find proteins for Q22A30 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL15
Go to UniProtKB:  Q22A30
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L5
BM, CM, EM, GM
301Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL5
Find proteins for Q231U7 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL5
Go to UniProtKB:  Q231U7
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RPL18
BN, CN, EN, GN
181Tetrahymena thermophilaMutation(s): 0 
Gene Names: RPL18
Find proteins for P0DJ17 (Tetrahymena thermophila)
Go to Gene View: RPL18
Go to UniProtKB:  P0DJ17
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
RPL19
BO, EO, GO
185Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL19
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL19
Go to UniProtKB:  P0DJ60
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L21
BP, CP, EP, GP
157Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL21
Find proteins for Q23TC8 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL21
Go to UniProtKB:  Q23TC8
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
RPL17
BQ, CQ, EQ, GQ
183Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL17
Find proteins for P0DJ16 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL17
Go to UniProtKB:  P0DJ16
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
RPL23A
BR, CR, ER, GR
150Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL23A (RPL25)
Find proteins for P0DJ57 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL23A
Go to UniProtKB:  P0DJ57
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
RPL26
BS, CS, ES, GS
135Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL26
Find proteins for Q23F79 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL26
Go to UniProtKB:  Q23F79
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
RPL24
BT, CT, ET, GT
158Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL24
Find proteins for P0DJ54 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL24
Go to UniProtKB:  P0DJ54
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
RPL35
BU, CU, EU, GU
124Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL35
Find proteins for P0DJ51 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL35
Go to UniProtKB:  P0DJ51
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)
Go to Gene View: RPL7
Go to UniProtKB:  P0DJ13
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L31
BW, CW, EW, GW
111Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL31
Find proteins for Q22DH9 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL31
Go to UniProtKB:  Q22DH9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L32
BX, CX, EX, GX
134Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL32
Find proteins for Q236T0 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL32
Go to UniProtKB:  Q236T0
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
RPL37A
BY, CY, EY, GY
103Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL37A (RPL43)
Find proteins for Q23G98 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL37A
Go to UniProtKB:  Q23G98
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
RPL19
CO
185Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Gene Names: RPL19
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
Go to Gene View: RPL19
Go to UniProtKB:  P0DJ60
Entity ID: 1
MoleculeChainsLengthOrganism
26S RRNAA1,D1,F1,H13354Tetrahymena thermophila
Entity ID: 20
MoleculeChainsLengthOrganism
5.8S RRNAB2,C2,E2,G2154Tetrahymena thermophila
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 SDF File 
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 SDF File 
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
BG, CG, CO, EG, GG
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 320.190α = 90.00
b = 289.250β = 91.22
c = 535.040γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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