6ZQG

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

90 S pre-ribosome transformation into the primordial 40 S subunit.

Cheng, J.Lau, B.La Venuta, G.Ameismeier, M.Berninghausen, O.Hurt, E.Beckmann, R.

(2020) Science 369: 1470-1476

  • DOI: https://doi.org/10.1126/science.abb4119
  • Primary Citation of Related Structures:  
    6ZQA, 6ZQB, 6ZQC, 6ZQD, 6ZQE, 6ZQF, 6ZQG

  • PubMed Abstract: 

    Production of small ribosomal subunits initially requires the formation of a 90 S precursor followed by an enigmatic process of restructuring into the primordial pre-40 S subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 S pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A 1 , thereby separating the 5'-external transcribed spacer (ETS) from 18 S ribosomal RNA. Next, the 5'-ETS and 90 S assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 S emerges, still retaining some 90 S factors including Dhr1, now ready to unwind the final small nucleolar U3-18 S RNA hybrid. Our data shed light on the elusive 90 S to pre-40 S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.


  • Organizational Affiliation

    Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14A [auth UB]810Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10B [auth UC]610Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Noc4,Nucleolar complex protein 4,Noc4C [auth US]552Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1D [auth UX]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4E [auth CJ]290Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10F [auth CK]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1G [auth CL]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinH [auth CM]367Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1I [auth JF],
J [auth JG]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1K [auth JH]483Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferaseL [auth JL]318Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.183
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1M [auth JJ]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pN [auth DF]225Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AO [auth DQ]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18P [auth DS]147Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AQ [auth DT]144Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AR [auth Dc]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AT [auth DA]255Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AU [auth DE]261Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AV [auth DG]236Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AW [auth DH]190Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AX [auth DI]200Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AY [auth DJ]197Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AZ [auth DL]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13AA [auth DN]151Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-ABA [auth DO]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-ACA [auth DZ]108Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-ADA [auth DW]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AEA [auth DX]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AFA [auth DY]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AGA [auth Db]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14HA [auth UN]899Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DHR1IA [auth JD]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 18
MoleculeChains LengthOrganismImage
18S rRNAS [auth D3]1,758Saccharomyces cerevisiae S288C
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Entity ID: 35
MoleculeChains LengthOrganismImage
U3 snoRNAJA [auth D4]23Saccharomyces cerevisiae S288C
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Entity ID: 36
MoleculeChains LengthOrganismImage
Poly-U RNAKA [auth D5]9Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
MA [auth CL]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
LA [auth UX]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth D3]
BB [auth D3]
CB [auth D3]
DB [auth D3]
EB [auth D3]
AB [auth D3],
BB [auth D3],
CB [auth D3],
DB [auth D3],
EB [auth D3],
FB [auth D3],
GB [auth D3],
HB [auth D3],
IB [auth D3],
JB [auth D3],
KB [auth D3],
LB [auth D3],
MB [auth D3],
NA [auth CL],
NB [auth D3],
OA [auth D3],
OB [auth D3],
PA [auth D3],
PB [auth D3],
QA [auth D3],
QB [auth D3],
RA [auth D3],
RB [auth D3],
SA [auth D3],
SB [auth D3],
TA [auth D3],
TB [auth D3],
UA [auth D3],
UB [auth D3],
VA [auth D3],
VB [auth D3],
WA [auth D3],
WB [auth D3],
XA [auth D3],
XB [auth D3],
YA [auth D3],
YB [auth D3],
ZA [auth D3],
ZB [auth DG]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references