6RBD

State 1 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism.

Mitterer, V.Shayan, R.Ferreira-Cerca, S.Murat, G.Enne, T.Rinaldi, D.Weigl, S.Omanic, H.Gleizes, P.E.Kressler, D.Plisson-Chastang, C.Pertschy, B.

(2019) Nat Commun 10: 2754-2754

  • DOI: 10.1038/s41467-019-10678-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-E ...

    Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps.


    Organizational Affiliation

    Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany. sebastien.ferreira-cerca@ur.de.,Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.,Biochemistry Centre, University of Heidelberg, 69120, Heidelberg, Germany.,Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland. dieter.kressler@unifr.ch.,Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria. brigitte.pertschy@uni-graz.at.,Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France. plisson@ibcg.biotoul.fr.,Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.,Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
b
82Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS27A
Go to UniProtKB:  P35997
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
e
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
A
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
B
255Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33442
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
C
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
E
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX35
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
G
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
H
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
I
200Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX39
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
J
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
L
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
N
151Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
V
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0V8
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
W
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
X
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX29
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
Y
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
c
67Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
d
56Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS29A (RPS36A, YS29A)
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41057
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Pre-rRNA-processing protein PNO1
h
274Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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: 21
MoleculeChainsSequence LengthOrganismDetails
Essential nuclear protein 1
i
483Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ENP1 (MEG1)
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38333
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein TSR1
k
788Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TSR1
Find proteins for Q07381 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: TSR1
Go to UniProtKB:  Q07381
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase RIO2
l
425Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RIO2
EC: 2.7.11.1
Find proteins for P40160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40160
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Dimethyladenosine transferase
y
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DIM1
EC: 2.1.1.183
Find proteins for P41819 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41819
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
F
225Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
M
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS12
Go to UniProtKB:  P48589
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
O
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS14A (CRY1, RPL59)
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06367
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
P
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
Q
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-A
R
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS17A (RP51A)
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02407
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
S
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX55
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
T
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS19A (RP55A, RPS16AA)
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07280
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
Z
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E792
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
D
240Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS3
Go to UniProtKB:  P05750
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
U
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS20
Go to UniProtKB:  P38701
Entity ID: 3
MoleculeChainsLengthOrganism
20S ribosomal RNA21801Saccharomyces cerevisiae S288C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceRIBOMAN

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Other
  • Version 1.3: 2020-01-22
    Type: Database references