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 1.1 of the entry. See complete history

Literature

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

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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S12
D
143 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S5
B
225 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S17-A
C
136 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S15
E
142 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S16-A
F
143 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S18-A
H
146 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S19-A
I
144 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S25-A
K
108 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S28-B
L
67 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
Ubiquitin-40S ribosomal protein S31
N
152 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S0-A
P
252 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S1-A
Q
255 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S2
R
254 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S4-A
S
261 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S6-A
T
236 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S7-A
U
190 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S8-A
V
200 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S9-A
W
197 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S11-A
X
156 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S13
Y
151 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S14-A
Z
137 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S21-A
a
87 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S22-A
b
130 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S23-A
c
145 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S24-A
d
135 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S27-A
f
82 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
Ribosome biogenesis protein TSR1
t
788 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
40S ribosomal protein S30-A
g
63 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
Pre-rRNA-processing protein PNO1
p
274 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
Serine/threonine-protein kinase RIO2
r
425 Saccharomyces 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
Molecule Chains Sequence Length Organism Details
Essential nuclear protein 1
e
483 Saccharomyces 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
Molecule Chains Length Organism
pre-18S ribosomal RNA 2 1800 Saccharomyces cerevisiae S288C
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
  • Version 1.1: 2018-02-21
    Type: Database references