5APO

Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and C-terminally tagged Rei1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation.

Greber, B.J.Gerhardy, S.Leitner, A.Leibundgut, M.Salem, M.Boehringer, D.Leulliot, N.Aebersold, R.Panse, V.G.Ban, N.

(2016) Cell 164: 91-102

  • DOI: https://doi.org/10.1016/j.cell.2015.11.027
  • Primary Citation of Related Structures:  
    5APN, 5APO

  • PubMed Abstract: 

    Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth A]254Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AF [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL6H [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AI [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AJ [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AK [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10L [auth I]221Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AM [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AN [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AO [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AP [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AQ [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AR [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AS [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AT [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AU [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AV [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AW [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AX [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AY [auth W]155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25Z [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AAA [auth Y]127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ABA [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28CA [auth a]149Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth b]59Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EA [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AFA [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GA [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AHA [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AIA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AJA [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-AKA [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ALA [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38MA [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39NA [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40OA [auth m]128Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-APA [auth o]106Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AQA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0RA [auth q]312Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Probable metalloprotease ARX1SA [auth x]616Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOPLASMIC 60S SUBUNIT BIOGENESIS FACTOR REI1TA [auth y]401Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
ALB1UA [auth z]95Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S ribosomal RNAA [auth 5]3,396Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 7]121Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAC [auth 8]158Saccharomyces cerevisiae S288C
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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 
OL [auth j]
PL [auth m]
QL [auth o]
RL [auth p]
SL [auth y]
OL [auth j],
PL [auth m],
QL [auth o],
RL [auth p],
SL [auth y],
TL [auth y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 5]
AC [auth 5]
AD [auth 5]
AE [auth 5]
AF [auth 5]
AB [auth 5],
AC [auth 5],
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 5],
AH [auth 5],
AI [auth 5],
AJ [auth 5],
AK [auth 5],
AL [auth 8],
BB [auth 5],
BC [auth 5],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 5],
BH [auth 5],
BI [auth 5],
BJ [auth 5],
BK [auth 5],
BL [auth 8],
CB [auth 5],
CC [auth 5],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 5],
CH [auth 5],
CI [auth 5],
CJ [auth 5],
CK [auth 5],
CL [auth 8],
DB [auth 5],
DC [auth 5],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth 5],
DH [auth 5],
DI [auth 5],
DJ [auth 5],
DK [auth 5],
DL [auth 8],
EB [auth 5],
EC [auth 5],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth 5],
EH [auth 5],
EI [auth 5],
EJ [auth 5],
EK [auth 5],
EL [auth 8],
FB [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth 5],
FH [auth 5],
FI [auth 5],
FJ [auth 5],
FK [auth 5],
FL [auth 8],
GB [auth 5],
GC [auth 5],
GD [auth 5],
GE [auth 5],
GF [auth 5],
GG [auth 5],
GH [auth 5],
GI [auth 5],
GJ [auth 5],
GK [auth 5],
GL [auth 8],
HB [auth 5],
HC [auth 5],
HD [auth 5],
HE [auth 5],
HF [auth 5],
HG [auth 5],
HH [auth 5],
HI [auth 5],
HJ [auth 5],
HK [auth 5],
HL [auth B],
IB [auth 5],
IC [auth 5],
ID [auth 5],
IE [auth 5],
IF [auth 5],
IG [auth 5],
IH [auth 5],
II [auth 5],
IJ [auth 5],
IK [auth 5],
IL [auth B],
JB [auth 5],
JC [auth 5],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth 5],
JH [auth 5],
JI [auth 5],
JJ [auth 5],
JK [auth 5],
JL [auth C],
KB [auth 5],
KC [auth 5],
KD [auth 5],
KE [auth 5],
KF [auth 5],
KG [auth 5],
KH [auth 5],
KI [auth 5],
KJ [auth 5],
KK [auth 5],
KL [auth N],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
LF [auth 5],
LG [auth 5],
LH [auth 5],
LI [auth 5],
LJ [auth 5],
LK [auth 5],
LL [auth P],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth 5],
MH [auth 5],
MI [auth 5],
MJ [auth 5],
MK [auth 5],
ML [auth R],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
NF [auth 5],
NG [auth 5],
NH [auth 5],
NI [auth 5],
NJ [auth 5],
NK [auth 5],
NL [auth V],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth 5],
OH [auth 5],
OI [auth 5],
OJ [auth 5],
OK [auth 5],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 5],
PG [auth 5],
PH [auth 5],
PI [auth 5],
PJ [auth 5],
PK [auth 5],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 5],
QG [auth 5],
QH [auth 5],
QI [auth 5],
QJ [auth 5],
QK [auth 5],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 5],
RG [auth 5],
RH [auth 5],
RI [auth 5],
RJ [auth 5],
RK [auth 5],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 5],
SG [auth 5],
SH [auth 5],
SI [auth 5],
SJ [auth 5],
SK [auth 5],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 5],
TG [auth 5],
TH [auth 5],
TI [auth 5],
TJ [auth 5],
TK [auth 5],
UB [auth 5],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
UG [auth 5],
UH [auth 5],
UI [auth 5],
UJ [auth 5],
UK [auth 7],
UL [auth y],
VA [auth 5],
VB [auth 5],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 5],
VG [auth 5],
VH [auth 5],
VI [auth 5],
VJ [auth 5],
VK [auth 7],
WA [auth 5],
WB [auth 5],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 5],
WG [auth 5],
WH [auth 5],
WI [auth 5],
WJ [auth 5],
WK [auth 7],
XA [auth 5],
XB [auth 5],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 5],
XG [auth 5],
XH [auth 5],
XI [auth 5],
XJ [auth 5],
XK [auth 7],
YA [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 5],
YG [auth 5],
YH [auth 5],
YI [auth 5],
YJ [auth 5],
YK [auth 7],
ZA [auth 5],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 5],
ZG [auth 5],
ZH [auth 5],
ZI [auth 5],
ZJ [auth 5],
ZK [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references, Other
  • Version 1.2: 2017-04-19
    Changes: Other
  • Version 1.3: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.4: 2019-12-18
    Changes: Other
  • Version 1.5: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary