6EML

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae.

Heuer, A.Thomson, E.Schmidt, C.Berninghausen, O.Becker, T.Hurt, E.Beckmann, R.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.30189

  • PubMed Abstract: 
  • Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resoluti ...

    Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resolution, revealing in molecular detail how assembly factors regulate the timely folding of pre-18S rRNA. The structure shows that, rather than sterically blocking 40S translational active sites, the associated assembly factors Tsr1, Enp1, Rio2 and Pno1 collectively preclude their final maturation, thereby preventing untimely tRNA and mRNA binding and error prone translation. Moreover, the structure explains how Pno1 coordinates the 3'end cleavage of the 18S rRNA by Nob1 and how the late factor's removal in the cytoplasm ensures the structural integrity of the maturing 40S subunit.


    Organizational Affiliation

    Gene Center Munich, Department of Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
D
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS12 
Go to UniProtKB:  P48589
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
B
225Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS5 (RPS2) 
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS5 
Go to UniProtKB:  P26783
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-A
C
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS17A (RP51A) 
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02407
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
E
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS15 (RPS21) 
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS15 
Go to UniProtKB:  Q01855
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
F
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS16A (RP61R) 
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX55
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
I
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS19A (RP55A,RPS16AA) 
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07280
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
K
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS25A (RPS31A) 
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E792
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-B
L
67Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS28B (RPS33B) 
Find proteins for P0C0X0 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0X0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
N
152Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS31 (RPS37,UBI3) 
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
P
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS0A (NAB1,NAB1A,YST1) 
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
Q
255Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS1A (PLC1,RPS10A) 
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33442
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
R
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS2 (RPS4,SUP38,SUP44) 
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS2 
Go to UniProtKB:  P25443
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
S
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS4A (RPS7B) 
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX35
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
T
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS6A (RPS101,RPS10B) 
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
U
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS7A (RPS30) 
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
V
200Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS8A (RPS14A) 
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX39
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
W
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS9A (RPS13A,YS11A) 
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
X
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS11A (RPS18A) 
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
Y
151Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS13 (RPS13C) 
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS13 
Go to UniProtKB:  P05756
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
Z
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS14A (CRY1,RPL59) 
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06367
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
a
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS21A (RPS25,RPS25A,RPS26A) 
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0V8
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
b
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS22A (RPS24,RPS24A) 
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
c
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS23A (RPS28A) 
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX29
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
d
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS24A (RPS24EA) 
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
f
82Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS27A 
Go to UniProtKB:  P35997
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein TSR1
t
788Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: TSR1
Find proteins for Q07381 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: TSR1 
Go to UniProtKB:  Q07381
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
g
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Pre-rRNA-processing protein PNO1
p
274Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PNO1 (DIM2,RRP20) 
Find proteins for Q99216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PNO1 
Go to UniProtKB:  Q99216
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase RIO2
r
425Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RIO2
EC: 2.7.11.1
Find proteins for P40160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40160
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Essential nuclear protein 1
e
483Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ENP1 (MEG1) 
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38333
Entity ID: 1
MoleculeChainsLengthOrganism
pre-18S ribosomal RNA21800N/A
Small Molecules
Modified Residues 4 Unique
IDChainsTypeFormula2D DiagramParent
U
Query on U
2
RNA LINKINGC9 H13 N2 O9 P

--

C
Query on C
2
RNA LINKINGC9 H14 N3 O8 P

--

A
Query on A
2
RNA LINKINGC10 H14 N5 O7 P

--

G
Query on G
2
RNA LINKINGC10 H14 N5 O8 P

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release