5JPQ

Cryo-EM structure of the 90S pre-ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome.

Kornprobst, M.Turk, M.Kellner, N.Cheng, J.Flemming, D.Kos-Braun, I.Kos, M.Thoms, M.Berninghausen, O.Beckmann, R.Hurt, E.

(2016) Cell 166: 380-393

  • DOI: 10.1016/j.cell.2016.06.014

  • PubMed Abstract: 
  • The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM stru ...

    The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.


    Organizational Affiliation

    Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD40 domain proteins
A, B, C, D, E, F, J, K, L, N, P, l, n
1290N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UTP10
G
1802Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S5L1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S5L1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UTP-A oligomerization domain
H
920N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 21
I
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: 5
MoleculeChainsSequence LengthOrganismDetails
WD40 domain proteins
M, O, m
870N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
UTP6
Q
456N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
UTP-B oligomerisation domain
R
560N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre mRNA splicing protein
S, T
412Sulfolobus solfataricusMutation(s): 0 
Find proteins for A0A0E3MJI1 (Sulfolobus solfataricus)
Go to UniProtKB:  A0A0E3MJI1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Snu13
U, V
130Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for P55858 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P55858
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Nop1
W, X
232Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: flpA
EC: 2.1.1.-
Find proteins for P58032 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P58032
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
rrp9
Y
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: 12
MoleculeChainsSequence LengthOrganismDetails
Rcl1
Z
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: 13
MoleculeChainsSequence LengthOrganismDetails
Bms1
a
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: 14
MoleculeChainsSequence LengthOrganismDetails
Imp3
b
183Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SDL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SDL4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Putative U3 small nucleolar ribonucleoprotein
c
297Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SE90 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SE90
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Utp24
d
184Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SE30 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SE30
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Emg1
e, f
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: 18
MoleculeChainsSequence LengthOrganismDetails
KRR1 small subunit processome component
g, h
322Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S3V7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S3V7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Kre33
i, j
1073Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Gene Names: NAT10
EC: 2.3.1.-
Find proteins for G0S273 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to Gene View: NAT10
Go to UniProtKB:  G0S273
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Utp30
k
391Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S7X0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S7X0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
eS1
o
265Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q23DE3 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q23DE3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
eS4
p
259Tetrahymena thermophilaMutation(s): 0 
Find proteins for P0C233 (Tetrahymena thermophila)
Go to UniProtKB:  P0C233
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uS7
q
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: 24
MoleculeChainsSequence LengthOrganismDetails
eS6
r
293Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for A4VD76 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  A4VD76
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eS7
s
197Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for I7MD19 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  I7MD19
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eS8
t
208Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22AV0 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22AV0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
uS4
u
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: 28
MoleculeChainsSequence LengthOrganismDetails
uS15
v
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: 29
MoleculeChainsSequence LengthOrganismDetails
uS11
w
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: 30
MoleculeChainsSequence LengthOrganismDetails
uS9
x
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: 31
MoleculeChainsSequence LengthOrganismDetails
uS17
y
157Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q22B78 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q22B78
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
uS8
z
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: 33
MoleculeChainsSequence LengthOrganismDetails
eS24
0
149Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for I7MAL3 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  I7MAL3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eS28
1
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: 35
MoleculeChainsLengthOrganism
18S ribosomal RNA21800Chaetomium thermophilum
Entity ID: 36
MoleculeChainsLengthOrganism
U3 RNA3274Chaetomium thermophilum
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C, D, E, F, H, J, K, l, L, m, M, N, n, O, P, Q, R
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.3 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: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Other
  • Version 1.2: 2017-07-05
    Type: Structure summary
  • Version 1.3: 2018-10-24
    Type: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Type: Advisory, Data collection, Derived calculations