4V8T

Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Cryo-Em Structures of Arx1 and Maturation Factors Rei1 and Jjj1 Bound to the 60S Ribosomal Subunit

Greber, B.J.Boehringer, D.Montellese, C.Ban, N.

(2012) Nat Struct Mol Biol 19: 1228

  • DOI: 10.1038/nsmb.2425
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 a ...

    Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 and late-maturation factors Rei1 and Jjj1 and determined their cryo-EM structures. Arx1 was visualized bound to the 60S subunit together with Rei1, at 8.1-Å resolution, to reveal the molecular details of Arx1 binding whereby Arx1 arrests the eukaryotic-specific rRNA expansion segment 27 near the polypeptide tunnel exit. Rei1 and Jjj1, which have been implicated in Arx1 recycling, bind in the vicinity of Arx1 and form a network of interactions. We suggest that, in addition to the role of Arx1 during pre-60S nuclear export, the binding of Arx1 conformationally locks the pre-60S subunit and inhibits the premature association of nascent chain-processing factors to the polypeptide tunnel exit.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L2-B
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: 2
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: 3
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: 4
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: 5
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L6-A
E
176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
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: 8
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L9-A
H
191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L10
I
221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L11-B
J
174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L12
K
155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L15-A
N
204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L16-A
O
199Saccharomyces cerevisiae S288CMutation(s): 20 
Gene Names: RPL16ARPL13RPL21AYIL133C
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L18-B
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: 18
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L19-B
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: 19
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L20-A
S
172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 20
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 L24-A
W
155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L25
X
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L26-A
Y
127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L27-A
Z
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L29
b
59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L32
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: 30
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: 31
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L30
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: 32
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L33-A
f
107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 33
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: 34
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: 35
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L36-A
i
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 36
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: 38
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L39
l
51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
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: 40
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L41-A
n
25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L42-A
o
106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ACIDIC RIBOSOMAL PROTEIN P0
q
312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN P1 ALPHA
r
47Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN P2 BETA
s
46Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
PROBABLE METALLOPROTEASE ARX1
t
614Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L13-A
L
199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
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 L17-A
P
184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L22-A
U
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L23-A
V
137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 27
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: 37
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L38
k
78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S RIBOSOMAL PROTEIN L43-A
p
92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 7
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: 47
MoleculeChainsLengthOrganism
ES27 OF THE 25S RRNA1114Saccharomyces cerevisiae S288C

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Entity ID: 49
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA7121Saccharomyces cerevisiae S288C

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Entity ID: 50
MoleculeChainsLengthOrganism
5.8S RIBOSOMAL RNA8158Saccharomyces cerevisiae S288C

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Entity ID: 48
MoleculeChainsLengthOrganism
25S RIBOSOMAL RNA53396Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
j, m, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-22
    Changes: Other
  • Version 1.3: 2017-08-02
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2018-03-07
    Changes: Source and taxonomy, Structure summary
  • Version 1.5: 2019-08-21
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.6: 2019-10-23
    Changes: Advisory, Data collection, Database references, Derived calculations