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 1.2 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: https://doi.org/10.1126/science.1211204
  • Primary Citation of Related Structures:  
    4V8P

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37B [auth AA],
KF [auth HA],
QD [auth FA],
WB [auth DA]
94Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPL39C [auth AB],
LF [auth HB],
RD [auth FB],
XB [auth DB]
52Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36AD [auth AC],
MF [auth HC],
SD [auth FC],
YB [auth DC]
109Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RPL6E [auth AE],
NF [auth HE],
TD [auth FE],
ZB [auth DE]
191Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RPL14AC [auth DF],
F [auth AF],
OF [auth HF],
UD [auth FF]
126Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RPL30BC [auth DG],
G [auth AG],
PF [auth HG],
VD [auth FG]
104Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RPL35ACC [auth DH],
H [auth AH],
QF [auth HH],
WD [auth FH]
113Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSLATION INITIATION FACTOR EIF-6, PUTATIVE FAMILY PROTEINDC [auth DJ],
I [auth AJ],
RF [auth HJ],
XD [auth FJ]
248Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40EC [auth DK],
J [auth AK],
SF [auth HK],
YD [auth FK]
129Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RPL34FC [auth DL],
K [auth AL],
TF [auth HL],
ZD [auth FL]
123Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22AE [auth FM],
GC [auth DM],
L [auth AM],
UF [auth HM]
118Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RPL27BE [auth FN],
HC [auth DN],
M [auth AN],
VF [auth HN]
144Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RPL28CE [auth FO],
IC [auth DO],
N [auth AO],
WF [auth HO]
134Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RPL38DE [auth FP],
JC [auth DP],
O [auth AP],
XF [auth HP]
89Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L36EE [auth FQ],
KC [auth DQ],
P [auth AQ],
YF [auth HQ]
104Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RPL29FE [auth FT],
LC [auth DT],
Q [auth AT],
ZF [auth HT]
66Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RPL13AG [auth HU],
GE [auth FU],
MC [auth DU],
R [auth AU]
206Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RPL18ABG [auth HX],
HE [auth FX],
NC [auth DX],
S [auth AX]
189Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RPL8KE [auth GA],
QC [auth EA],
V [auth BA],
WA [auth CA]
264Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3LE [auth GB],
RC [auth EB],
W [auth BB],
XA [auth CB]
391Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RPL4ME [auth GC],
SC [auth EC],
X [auth BC],
YA [auth CC]
410Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11NE [auth GD],
TC [auth ED],
Y [auth BD],
ZA [auth CD]
172Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L9AB [auth CE],
OE [auth GE],
UC [auth EE],
Z [auth BE]
188Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RPL7AAA [auth BF],
BB [auth CF],
PE [auth GF],
VC [auth EF]
255Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RPLP0BA [auth BG],
CB [auth CG],
QE [auth GG],
WC [auth EG]
123Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10CA [auth BH],
DB [auth CH],
RE [auth GH],
XC [auth EH]
215Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13ADA [auth BI],
EB [auth CI],
SE [auth GI],
YC [auth EI]
198Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RPL23EA [auth BJ],
FB [auth CJ],
TE [auth GJ],
ZC [auth EJ]
141Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27AAD [auth EK],
FA [auth BK],
GB [auth CK],
UE [auth GK]
149Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15BD [auth EL],
GA [auth BL],
HB [auth CL],
VE [auth GL]
204Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L5CD [auth EM],
HA [auth BM],
IB [auth CM],
WE [auth GM]
301Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RPL18DD [auth EN],
IA [auth BN],
JB [auth CN],
XE [auth GN]
181Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RPL19ED [auth EO],
JA [auth BO],
YE [auth GO]
185Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L21FD [auth EP],
KA [auth BP],
LB [auth CP],
ZE [auth GP]
157Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
RPL17AF [auth GQ],
GD [auth EQ],
LA [auth BQ],
MB [auth CQ]
183Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
RPL23ABF [auth GR],
HD [auth ER],
MA [auth BR],
NB [auth CR]
150Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
RPL26CF [auth GS],
ID [auth ES],
NA [auth BS],
OB [auth CS]
135Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24DF [auth GT],
JD [auth ET],
OA [auth BT],
PB [auth CT]
158Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
RPL35EF [auth GU],
KD [auth EU],
PA [auth BU],
QB [auth CU]
124Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7FF [auth GV],
LD [auth EV],
QA [auth BV],
RB [auth CV]
239Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L31GF [auth GW],
MD [auth EW],
RA [auth BW],
SB [auth CW]
111Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q22DH9 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ22DH9
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L32HF [auth GX],
ND [auth EX],
SA [auth BX],
TB [auth CX]
134Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q236T0 (Tetrahymena thermophila (strain SB210))
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UniProt GroupQ236T0
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
RPL37AIF [auth GY],
OD [auth EY],
TA [auth BY],
UB [auth CY]
103Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for Q23G98 (Tetrahymena thermophila (strain SB210))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
RPL19KB [auth CO]185Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for P0DJ60 (Tetrahymena thermophila (strain SB210))
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Entity ID: 1
MoleculeChains LengthOrganismImage
26S RRNAA [auth A1],
JF [auth H1],
PD [auth F1],
VB [auth D1]
3,354Tetrahymena thermophila
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Entity ID: 20
MoleculeChains LengthOrganismImage
5.8S RRNAIE [auth G2],
OC [auth E2],
T [auth B2],
UA [auth C2]
154Tetrahymena thermophila
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Entity ID: 21
MoleculeChains LengthOrganismImage
5S RRNAJE [auth G3],
PC [auth E3],
U [auth B3],
VA [auth C3]
120Tetrahymena thermophila
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AO [auth AL]
AOA [auth HK]
BHA [auth FK]
BOA [auth HL]
CHA [auth FL]
AO [auth AL],
AOA [auth HK],
BHA [auth FK],
BOA [auth HL],
CHA [auth FL],
QP [auth CY],
RY [auth DA],
SY [auth DC],
TO [auth BY],
TZ [auth EY],
UN [auth AA],
VY [auth DK],
WY [auth DL],
XN [auth AC],
YGA [auth FA],
YHA [auth GY],
YN [auth AK],
YNA [auth HA],
ZGA [auth FC],
ZNA [auth HC]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AAA [auth F1]
ABA [auth F1]
ACA [auth F1]
ADA [auth F1]
AEA [auth F1]
AAA [auth F1],
ABA [auth F1],
ACA [auth F1],
ADA [auth F1],
AEA [auth F1],
AFA [auth F1],
AGA [auth F1],
AH [auth A1],
AHA [auth FK],
AI [auth A1],
AIA [auth H1],
AJ [auth A1],
AJA [auth H1],
AK [auth A1],
AKA [auth H1],
AL [auth A1],
ALA [auth H1],
AM [auth A1],
AMA [auth H1],
AN [auth A1],
ANA [auth H1],
AP [auth C3],
AQ [auth D1],
AR [auth D1],
AS [auth D1],
AT [auth D1],
AU [auth D1],
AV [auth D1],
AW [auth D1],
AX [auth D1],
AY [auth D1],
AZ [auth E2],
BAA [auth F1],
BBA [auth F1],
BCA [auth F1],
BDA [auth F1],
BEA [auth F1],
BFA [auth F1],
BGA [auth F1],
BH [auth A1],
BI [auth A1],
BIA [auth H1],
BJ [auth A1],
BJA [auth H1],
BK [auth A1],
BKA [auth H1],
BL [auth A1],
BLA [auth H1],
BM [auth A1],
BMA [auth H1],
BN [auth A1],
BNA [auth H1],
BO [auth B2],
BP [auth C3],
BQ [auth D1],
BR [auth D1],
BS [auth D1],
BT [auth D1],
BU [auth D1],
BV [auth D1],
BW [auth D1],
BX [auth D1],
BY [auth D1],
BZ [auth E2],
CAA [auth F1],
CBA [auth F1],
CCA [auth F1],
CDA [auth F1],
CEA [auth F1],
CFA [auth F1],
CG [auth A1],
CGA [auth F1],
CH [auth A1],
CI [auth A1],
CIA [auth H1],
CJ [auth A1],
CJA [auth H1],
CK [auth A1],
CKA [auth H1],
CL [auth A1],
CLA [auth H1],
CM [auth A1],
CMA [auth H1],
CN [auth A1],
CNA [auth H1],
CO [auth B2],
COA [auth HT],
CP [auth C3],
CQ [auth D1],
CR [auth D1],
CS [auth D1],
CT [auth D1],
CU [auth D1],
CV [auth D1],
CW [auth D1],
CX [auth D1],
CY [auth D1],
CZ [auth E2],
DAA [auth F1],
DBA [auth F1],
DCA [auth F1],
DDA [auth F1],
DEA [auth F1],
DFA [auth F1],
DG [auth A1],
DGA [auth F1],
DH [auth A1],
DHA [auth FT],
DI [auth A1],
DIA [auth H1],
DJ [auth A1],
DJA [auth H1],
DK [auth A1],
DKA [auth H1],
DL [auth A1],
DLA [auth H1],
DM [auth A1],
DMA [auth H1],
DN [auth A1],
DNA [auth H1],
DO [auth B2],
DP [auth C3],
DQ [auth D1],
DR [auth D1],
DS [auth D1],
DT [auth D1],
DU [auth D1],
DV [auth D1],
DW [auth D1],
DX [auth D1],
DY [auth D1],
DZ [auth E2],
EAA [auth F1],
EBA [auth F1],
ECA [auth F1],
EDA [auth F1],
EEA [auth F1],
EFA [auth F1],
EG [auth A1],
EGA [auth F1],
EH [auth A1],
EHA [auth G2],
EI [auth A1],
EIA [auth H1],
EJ [auth A1],
EJA [auth H1],
EK [auth A1],
EKA [auth H1],
EL [auth A1],
ELA [auth H1],
EM [auth A1],
EMA [auth H1],
EN [auth A1],
ENA [auth H1],
EO [auth B2],
EP [auth C3],
EQ [auth D1],
ER [auth D1],
ES [auth D1],
ET [auth D1],
EU [auth D1],
EV [auth D1],
EW [auth D1],
EX [auth D1],
EY [auth D1],
EZ [auth E2],
FAA [auth F1],
FBA [auth F1],
FCA [auth F1],
FDA [auth F1],
FEA [auth F1],
FFA [auth F1],
FG [auth A1],
FGA [auth F1],
FH [auth A1],
FHA [auth G2],
FI [auth A1],
FIA [auth H1],
FJ [auth A1],
FJA [auth H1],
FK [auth A1],
FKA [auth H1],
FL [auth A1],
FLA [auth H1],
FM [auth A1],
FMA [auth H1],
FN [auth A1],
FNA [auth H1],
FO [auth B2],
FP [auth C3],
FQ [auth D1],
FR [auth D1],
FS [auth D1],
FT [auth D1],
FU [auth D1],
FV [auth D1],
FW [auth D1],
FX [auth D1],
FY [auth D1],
FZ [auth E3],
GAA [auth F1],
GBA [auth F1],
GCA [auth F1],
GDA [auth F1],
GEA [auth F1],
GFA [auth F1],
GG [auth A1],
GGA [auth F1],
GH [auth A1],
GHA [auth G2],
GI [auth A1],
GIA [auth H1],
GJ [auth A1],
GJA [auth H1],
GK [auth A1],
GKA [auth H1],
GL [auth A1],
GLA [auth H1],
GM [auth A1],
GMA [auth H1],
GN [auth A1],
GNA [auth