5JPQ

Cryo-EM structure of the 90S pre-ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 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
  • Primary Citation of Related Structures:  
    5JPQ

  • 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 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 ...

    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. Electronic address: ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WD40 domain proteins
A, B, C, D, E, F, J, K
A, B, C, D, E, F, J, K, L, N, P, LA [auth l], NA [auth n]
1290Chaetomium thermophilumMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UTP10G1802Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S5L1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UTP-A oligomerization domainH920Chaetomium thermophilumMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21I939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
WD40 domain proteinsM, O, MA [auth m]870Chaetomium thermophilumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
UTP6Q456Chaetomium thermophilumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UTP-B oligomerisation domainR560Chaetomium thermophilumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre mRNA splicing proteinS, T412Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Snu13U, V130Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for P55858 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 10
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Nop1W, X232Chaetomium thermophilumMutation(s): 0 
EC: 2.1.1
UniProt
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Entity ID: 11
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rrp9Y573Chaetomium thermophilumMutation(s): 0 
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Entity ID: 12
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Rcl1Z367Chaetomium thermophilumMutation(s): 0 
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Entity ID: 13
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Bms1AA [auth a]1183Chaetomium thermophilumMutation(s): 0 
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Entity ID: 14
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Imp3BA [auth b]183Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SDL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 15
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Putative U3 small nucleolar ribonucleoproteinCA [auth c]297Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SE90 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Utp24DA [auth d]184Chaetomium thermophilumMutation(s): 0 
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Entity ID: 17
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Emg1EA [auth e], FA [auth f]252Chaetomium thermophilumMutation(s): 0 
EC: 2.1.1.260
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Entity ID: 18
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KRR1 small subunit processome componentGA [auth g], HA [auth h]322Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 19
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Kre33IA [auth i], JA [auth j]1073Chaetomium thermophilumMutation(s): 0 
EC: 2.3.1
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Entity ID: 20
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Utp30KA [auth k]391Chaetomium thermophilumMutation(s): 0 
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Entity ID: 21
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eS1OA [auth o]265Chaetomium thermophilumMutation(s): 0 
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Entity ID: 22
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eS4PA [auth p]259Chaetomium thermophilumMutation(s): 0 
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Entity ID: 23
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uS7QA [auth q]225Chaetomium thermophilumMutation(s): 0 
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Entity ID: 24
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eS6RA [auth r]293Chaetomium thermophilumMutation(s): 0 
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Entity ID: 25
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eS7SA [auth s]197Chaetomium thermophilumMutation(s): 0 
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Entity ID: 26
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eS8TA [auth t]208Chaetomium thermophilumMutation(s): 0 
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Entity ID: 27
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uS4UA [auth u]197Chaetomium thermophilumMutation(s): 0 
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Entity ID: 28
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uS15VA [auth v]151Chaetomium thermophilumMutation(s): 0 
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Entity ID: 29
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uS11WA [auth w]137Chaetomium thermophilumMutation(s): 0 
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Entity ID: 30
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uS9XA [auth x]143Chaetomium thermophilumMutation(s): 0 
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Entity ID: 31
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uS17YA [auth y]157Chaetomium thermophilumMutation(s): 0 
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Entity ID: 32
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uS8ZA [auth z]130Chaetomium thermophilumMutation(s): 0 
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Entity ID: 33
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eS24AB [auth 0]149Chaetomium thermophilumMutation(s): 0 
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Entity ID: 34
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eS28BB [auth 1]67Chaetomium thermophilumMutation(s): 0 
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Entity ID: 35
MoleculeChainsLengthOrganismImage
18S ribosomal RNACB [auth 2]1800Chaetomium thermophilum
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Entity ID: 36
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U3 RNADB [auth 3]274Chaetomium thermophilum
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Other
  • Version 1.2: 2017-07-05
    Changes: Structure summary
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.6: 2020-03-11
    Changes: Source and taxonomy