5OQL

Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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

3.2- angstrom -resolution structure of the 90S preribosome before A1 pre-rRNA cleavage.

Cheng, J.Kellner, N.Berninghausen, O.Hurt, E.Beckmann, R.

(2017) Nat. Struct. Mol. Biol. 24: 954-964

  • DOI: 10.1038/nsmb.3476

  • PubMed Abstract: 
  • The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophi ...

    The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.


    Organizational Affiliation

    Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periodic tryptophan protein 2-like protein
A
904Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SF93 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SF93
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Utp2
B
907Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SDW0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SDW0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Utp3
C
648Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S4H3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S4H3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Utp4
D
884Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SCT7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SCT7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Utp6
E
414Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S387 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S387
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Utp7
F
558Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RZ99 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RZ99
Entity ID: 7
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: 8
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 11
H
270Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Gene Names: UTP11
Find proteins for G0SF32 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to Gene View: UTP11
Go to UniProtKB:  G0SF32
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Utp12
I
962Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RZL9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RZL9
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Utp13
J
912Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SG95 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SG95
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Utp14
K
938Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S8Y4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S8Y4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Utp15
L
557Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SEI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SEI5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Utp17
M
960Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SCS8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SCS8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Utp18
N
618Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SBN9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SBN9
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Putative U3 snoRNP protein
O
1049Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S872 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S872
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Utp24
P
194Chaetomium 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
Utp30
Q
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: 18
MoleculeChainsSequence LengthOrganismDetails
Nop1
R, S
313Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SGY2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SGY2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Putative nucleolar protein
T
523Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S2U4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S2U4
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Nop58
U
582Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RYF6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYF6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Snu13
V, W
127Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SGM0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SGM0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Rrp9
X
630Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SG51 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SG51
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RNA 3'-terminal phosphate cyclase-like protein
Y
411Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S0B1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S0B1
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Bms1
Z
1163Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S445 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S445
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Imp3
a
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: 26
MoleculeChainsSequence LengthOrganismDetails
Putative U3 small nucleolar ribonucleoprotein
b
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: 27
MoleculeChainsSequence LengthOrganismDetails
Putative U3 small nucleolar ribonucleoprotein protein
c
785Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S9I7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S9I7
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Sof1
d
446Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RY94 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY94
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Emg1
e, f
252Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SAY9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SAY9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
KRR1 small subunit processome component
g
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: 31
MoleculeChainsSequence LengthOrganismDetails
Pre-rRNA-processing protein PNO1
h
259Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Gene Names: PNO1 (DIM2)
Find proteins for G0S3T2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to Gene View: PNO1
Go to UniProtKB:  G0S3T2
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
RNA cytidine acetyltransferase
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: 33
MoleculeChainsSequence LengthOrganismDetails
Fcf2
k
203Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S4E3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S4E3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1
l
255Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Gene Names: RPS1
Find proteins for G0S7T8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S7T8
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4
m
264Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S1A6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S1A6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein s5-like protein
n
212Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S1Z0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S1Z0
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
o
239Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RY43 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY43
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-like protein
p
203Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S8C4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S8C4
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
q
202Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RY45 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY45
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein s9-like protein
r
190Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S0Z4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S0Z4
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13-like protein
s
151Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RZM9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RZM9
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-like protein
t
150Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SFL1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SFL1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-like protein
u
143Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SBR7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SBR7
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-like protein
v
161Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SF00 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SF00
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-like protein
w
130Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SHI0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SHI0
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein s23-like protein
x
145Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RY17 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY17
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
y
136Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for P0CU28 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  P0CU28
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-like protein
z
68Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S9M9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S9M9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Faf1
0
311Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S5F1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S5F1
Entity ID: 50
MoleculeChainsLengthOrganism
35S rRNA12568Chaetomium thermophilum var. thermophilum DSM 1495
Entity ID: 51
MoleculeChainsLengthOrganism
U3 snoRNA2274Chaetomium thermophilum var. thermophilum DSM 1495
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
P
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references