6FAI

Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit.

Scaiola, A.Pena, C.Weisser, M.Bohringer, D.Leibundgut, M.Klingauf-Nerurkar, P.Gerhardy, S.Panse, V.G.Ban, N.

(2018) EMBO J 37

  • DOI: 10.15252/embj.201798499
  • Primary Citation of Related Structures:  
    6FAI

  • PubMed Abstract: 
  • Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation ...

    Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland vpanse@imm.uzh.ch ban@mol.biol.ethz.ch.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-AA [auth b]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35997 
Go to UniProtKB:  P35997
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-AB [auth c]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E7X9 
Go to UniProtKB:  Q3E7X9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-AC [auth d]56Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41057 
Go to UniProtKB:  P41057
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-AD [auth e]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX33 
Go to UniProtKB:  P0CX33
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinE [auth g]319Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
UniProt
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38011 
Go to UniProtKB:  P38011
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1F [auth h]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
UniProt
Find proteins for Q99216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99216 
Go to UniProtKB:  Q99216
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Essential nuclear protein 1G [auth i]483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
UniProt
Find proteins for P38333 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38333 
Go to UniProtKB:  P38333
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LTV1H [auth j]463Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LTV1YKL143WYKL2
UniProt
Find proteins for P34078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34078 
Go to UniProtKB:  P34078
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein TSR1I [auth k]788Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TSR1YDL060W
UniProt
Find proteins for Q07381 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07381 
Go to UniProtKB:  Q07381
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase RIO2J [auth l]425Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIO2YNL207WN1342
EC: 2.7.11.1
UniProt
Find proteins for P40160 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40160 
Go to UniProtKB:  P40160
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AL [auth A]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
UniProt
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32905 
Go to UniProtKB:  P32905
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-AM [auth B]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33442 
Go to UniProtKB:  P33442
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2N [auth C]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
UniProt
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25443 
Go to UniProtKB:  P25443
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3O [auth D]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05750 
Go to UniProtKB:  P05750
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-AP [auth E]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX35 
Go to UniProtKB:  P0CX35
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5Q [auth F]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26783 
Go to UniProtKB:  P26783
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-AR [auth G]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX37 
Go to UniProtKB:  P0CX37
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-AS [auth H]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26786 
Go to UniProtKB:  P26786
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8-AT [auth I]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
UniProt
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX39 
Go to UniProtKB:  P0CX39
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-AU [auth J]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O13516 
Go to UniProtKB:  O13516
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-AV [auth L]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
UniProt
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX47 
Go to UniProtKB:  P0CX47
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12W [auth M]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
UniProt
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48589 
Go to UniProtKB:  P48589
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13X [auth N]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05756 
Go to UniProtKB:  P05756
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-AY [auth O]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
UniProt
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06367 
Go to UniProtKB:  P06367
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15Z [auth P]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01855 
Go to UniProtKB:  Q01855
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-AAA [auth Q]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX51 
Go to UniProtKB:  P0CX51
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-ABA [auth R]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
UniProt
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02407 
Go to UniProtKB:  P02407
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-ACA [auth S]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX55 
Go to UniProtKB:  P0CX55
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-ADA [auth T]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07280 
Go to UniProtKB:  P07280
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20EA [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
UniProt
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38701 
Go to UniProtKB:  P38701
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-AFA [auth V]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
UniProt
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C0V8 
Go to UniProtKB:  P0C0V8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AGA [auth W]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C0W1 
Go to UniProtKB:  P0C0W1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-AHA [auth X]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX29 
Go to UniProtKB:  P0CX29
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-AIA [auth Y]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX31 
Go to UniProtKB:  P0CX31
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-AJA [auth Z]108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E792 
Go to UniProtKB:  Q3E792
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsLengthOrganismImage
20S ribosomal RNAK [auth 2]1800Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
KA [auth b], LA [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2] , AC [auth 2] , BB [auth 2] , BC [auth 2] , CB [auth 2] , CC [auth 2] , DB [auth 2] , DC [auth 2] , 
AB [auth 2],  AC [auth 2],  BB [auth 2],  BC [auth 2],  CB [auth 2],  CC [auth 2],  DB [auth 2],  DC [auth 2],  EB [auth 2],  EC [auth 2],  FB [auth 2],  FC [auth 2],  GB [auth 2],  HB [auth 2],  IB [auth 2],  JB [auth 2],  KB [auth 2],  LB [auth 2],  MA [auth 2],  MB [auth 2],  NA [auth 2],  NB [auth 2],  OA [auth 2],  OB [auth 2],  PA [auth 2],  PB [auth 2],  QA [auth 2],  QB [auth 2],  RA [auth 2],  RB [auth 2],  SA [auth 2],  SB [auth 2],  TA [auth 2],  TB [auth 2],  UA [auth 2],  UB [auth 2],  VA [auth 2],  VB [auth 2],  WA [auth 2],  WB [auth 2],  XA [auth 2],  XB [auth 2],  YA [auth 2],  YB [auth 2],  ZA [auth 2],  ZB [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references