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 1.4 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: 10.1016/j.cell.2015.11.027
  • Structures With Same Primary Citation

  • 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 center ...

    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. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
A
254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
C
362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN EL6
E
176Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
F
244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
G
256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
H
191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
I
221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
L
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M
138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
N
204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
O
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
P
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
Q
186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
R
189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
S
172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
T
160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
U
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
W
155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
X
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
Y
127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
a
149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
c
105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
d
113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
e
130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
f
107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
g
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
h
120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
i
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
j
88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
k
78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
l
51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
m
128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
o
106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
p
92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
q
312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Probable metalloprotease ARX1
x
616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ARX1YDR101CYD8557.10c
EC: 3
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
CYTOPLASMIC 60S SUBUNIT BIOGENESIS FACTOR REI1
y
401Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ALB1
z
95Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
J
174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
V
137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
Z
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNA53396Saccharomyces cerevisiae S288C

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA7121Saccharomyces cerevisiae S288C

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8158Saccharomyces cerevisiae S288C
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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j, m, o, p, y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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5, 7, 8, B, C, N, P, R, V, y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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