5WYK

Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 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

Molecular architecture of the 90S small subunit pre-ribosome.

Sun, Q.Zhu, X.Qi, J.An, W.Lan, P.Tan, D.Chen, R.Wang, B.Zheng, S.Zhang, C.Chen, X.Zhang, W.Chen, J.Dong, M.Q.Ye, K.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.22086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of <i>Saccharomyces cere ...

    Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China.,PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
rRNA 2'-O-methyltransferase fibrillarin
3B, 3C
327Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOP1 (LOT3)
EC: 2.1.1.-
Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P15646
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 56
3D
504Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOP56 (SIK1)
Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NOP56
Go to UniProtKB:  Q12460
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 58
3E
511Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NOP58 (NOP5)
Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NOP58
Go to UniProtKB:  Q12499
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 9
3F
573Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP9
Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RRP9
Go to UniProtKB:  Q06506
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein
3G, 3H
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SNU13
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SNU13
Go to UniProtKB:  P39990
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Utp4
AA
776N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Utp5
AB
643N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Utp8
AC
713N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Utp9
AD
575N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 10
AE
1769Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP10
Find proteins for P42945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P42945
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Utp15
AF
513N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Utp17
AG
896N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BMS1
B1
1183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BMS1
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BMS1
Go to UniProtKB:  Q08965
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Periodic tryptophan protein 2
BA
923Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PWP2 (UTP1)
Find proteins for P25635 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PWP2
Go to UniProtKB:  P25635
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 12
BB
943Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DIP2 (UTP12)
Find proteins for Q12220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12220
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 13
BC
817Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP13
Find proteins for Q05946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05946
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 18
BD
594Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP18
Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: UTP18
Go to UniProtKB:  P40362
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 21
BE
939Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP21
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06078
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 7
CA
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RRP7
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25368
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 22
CB
1237Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP22
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53254
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA small subunit methyltransferase NEP1
E1, E2
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EMG1 (NEP1)
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: EMG1
Go to UniProtKB:  Q06287
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Enp2
E4
707N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
KRR1 small subunit processome component
K1
316Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: KRR1
Find proteins for P25586 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: KRR1
Go to UniProtKB:  P25586
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar ribonucleoprotein protein IMP3
MA
183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IMP3
Find proteins for P32899 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32899
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar ribonucleoprotein protein IMP4
MB
290Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IMP4
Find proteins for P53941 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: IMP4
Go to UniProtKB:  P53941
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Mpp10,U3 small nucleolar RNA-associated protein MPP10
MC
593Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MPP10
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47083
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-rRNA-processing protein PNO1
P1
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: 30
MoleculeChainsSequence LengthOrganismDetails
RNA 3'-terminal phosphate cyclase-like protein
R1
367Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RCL1 (RTC1)
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RCL1
Go to UniProtKB:  Q08096
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Sof1
S1
489N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
SC
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: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
SF
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: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
SG
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: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
SI
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: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
SJ
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: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
SK
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: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
SM
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: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
SO
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: 41
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
SP
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: 42
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
SR
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: 43
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
SX
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: 44
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
SY
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: 45
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
SZ
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: 46
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
Sc
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: 47
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
Sd
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: 48
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
Sf
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: 49
MoleculeChainsSequence LengthOrganismDetails
Utp7
U1
554N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Utp11
U2
250N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein FCF1
U4
189Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: FCF1
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: FCF1
Go to UniProtKB:  Q05498
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein UTP30
U5
274Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UTP30
Find proteins for P36144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36144
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Helical domain protein
UA
1615N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Helical domain protein
UB
987N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Unassigned helices
UC
1033N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
U3 RNA3A333Saccharomyces cerevisiae S288C
Entity ID: 7
MoleculeChainsLengthOrganism
5ETS RNA5A700Saccharomyces cerevisiae S288C
Entity ID: 32
MoleculeChainsLengthOrganism
18S ribosomal RNASA1812Saccharomyces cerevisiae S288C
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
AA, AB, AC, AD, AF, AG, E4, MC, S1, U1, U2, UA, UB, UC
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-13 
  • Released Date: 2017-03-29 
  • Deposition Author(s): Ye, K., Zhu, X., Sun, Q.

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Structure summary