6RXU

Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1


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

Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration.

Cheng, J.Bassler, J.Fischer, P.Lau, B.Kellner, N.Kunze, R.Griesel, S.Kallas, M.Berninghausen, O.Strauss, D.Beckmann, R.Hurt, E.

(2019) Mol Cell 75: 1256-1269.e7

  • DOI: 10.1016/j.molcel.2019.06.032
  • Primary Citation of Related Structures:  
    6RXU, 6RXT, 6RXV, 6RXY, 6RXX, 6RXZ

  • PubMed Abstract: 
  • Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5' > 3', but this directionality may not be accurate ...

    Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5' > 3', but this directionality may not be accurate. Here, by analyzing the structure of a series of 90S assembly intermediates from Chaetomium thermophilum, we discover a reverse order of 18S rRNA subdomain incorporation. Large parts of the 18S rRNA 3' and central domains assemble first into the 90S before the 5' domain is integrated. This final incorporation depends on a contact between a heterotrimer Enp2-Bfr2-Lcp5 recruited to the flexible 5' domain and Kre33, which reconstitutes the Kre33-Enp-Brf2-Lcp5 module on the compacted 90S. Keeping the 5' domain temporarily segregated from the 90S scaffold could provide extra time to complete the multifaceted 5' domain folding, which depends on a distinct set of snoRNAs and processing factors.


    Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany. Electronic address: ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2-like proteinA [auth UA]904Chaetomium thermophilumMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Utp2B [auth UB]907Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Utp3C [auth UC]648Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S4H3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Utp4D [auth UD]884Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Utp6E [auth UF]414Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S387 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Utp7F [auth UG]558Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0RZ99 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UTP10G [auth UJ]1802Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11H [auth UK]270Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Utp12I [auth UL]962Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0RZL9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Utp13J [auth UM]912Chaetomium thermophilumMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Utp14K [auth UN]938Chaetomium thermophilumMutation(s): 0 
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Find proteins for G0S8Y4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 12
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Utp15L [auth UO]557Chaetomium thermophilumMutation(s): 0 
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Find proteins for G0SEI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Utp17M [auth UQ]960Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SCS8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Utp18N [auth UR]618Chaetomium thermophilumMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 snoRNP proteinO [auth UU]1049Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S872 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 16
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Utp24P [auth UX]193Chaetomium thermophilumMutation(s): 0 
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Entity ID: 17
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Utp30Q [auth UZ]391Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S7X0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 18
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Nop1R [auth CA], S [auth CB]313Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SGY2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Nop56T [auth CC]523Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S2U4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Nop58U [auth CD]582Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0RYF6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Snu13V [auth CE], W [auth CF]127Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SGM0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Rrp9X [auth CG]630Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SG51 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 23
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RNA 3'-terminal phosphate cyclase-like proteinY [auth CH]411Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S0B1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Bms1Z [auth CI]1163Chaetomium thermophilumMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Imp3AA [auth CJ]183Chaetomium thermophilumMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoproteinBA [auth CK]297Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoprotein proteinCA [auth CL]785Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Sof1DA [auth CM]446Chaetomium thermophilumMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Emg1EA [auth CN], FA [auth CO]252Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
KRR1 small subunit processome componentGA [auth CP]322Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S3V7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 31
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Pre-rRNA-processing protein PNO1HA [auth CQ]259Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Kre33IA [auth CR], JA [auth CS]1073Chaetomium thermophilumMutation(s): 0 
EC: 2.3.1
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Find proteins for G0S273 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Fcf2KA [auth CT]203Chaetomium thermophilumMutation(s): 0 
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Entity ID: 34
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40S ribosomal protein S1LA [auth Ca]255Chaetomium thermophilumMutation(s): 0 
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Entity ID: 35
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40S ribosomal protein S4MA [auth Cb]264Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S1A6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 36
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40S ribosomal protein s5-like proteinNA [auth Cc]212Chaetomium thermophilumMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6OA [auth Cd]239Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 38
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40S ribosomal protein S7PA [auth Ce]203Chaetomium thermophilumMutation(s): 0 
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Entity ID: 39
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40S ribosomal protein S8QA [auth Cf]202Chaetomium thermophilumMutation(s): 0 
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Entity ID: 40
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40S ribosomal protein s9-like proteinRA [auth Cg]190Chaetomium thermophilumMutation(s): 0 
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Entity ID: 41
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40S ribosomal protein S13-like proteinSA [auth Ch]151Chaetomium thermophilumMutation(s): 0 
UniProt
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Entity ID: 42
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40S ribosomal protein S14-like proteinTA [auth Ci]150Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SFL1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 43
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40S ribosomal protein S16-like proteinUA [auth Cj]143Chaetomium thermophilumMutation(s): 0 
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Entity ID: 44
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40S ribosomal protein S11-like proteinVA [auth Ck]161Chaetomium thermophilumMutation(s): 0 
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Entity ID: 45
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40S ribosomal protein S22-like proteinWA [auth Cm]130Chaetomium thermophilumMutation(s): 0 
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Entity ID: 46
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40S ribosomal protein s23-like proteinXA [auth Cn]145Chaetomium thermophilumMutation(s): 0 
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Entity ID: 47
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40S ribosomal protein S24YA [auth Co]136Chaetomium thermophilumMutation(s): 0 
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Entity ID: 48
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40S ribosomal protein S28-like proteinZA [auth Cp]68Chaetomium thermophilumMutation(s): 0 
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Find proteins for G0S9M9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 49
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Faf1AB [auth CU]311Chaetomium thermophilumMutation(s): 0 
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Entity ID: 52
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Ribosome biogenesis protein ENP2DB [auth CW]668Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S902 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 53
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Utp20EB [auth UT]2612Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SHP3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 54
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Utp8FB [auth UH]930Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for P0CT47 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Utp5GB [auth UE], MB [auth UI]410Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0RYX2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Noc4HB [auth US]549Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0RZL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ribosomal proteinIB [auth Cl]156Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S6J7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Enp1JB [auth CX]480Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S5J4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein lcp5-like proteinKB [auth CY]381Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S7Z2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
Bfr2LB [auth CZ]609Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0SAJ6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Utp16NB [auth UP]364Chaetomium thermophilumMutation(s): 0 
UniProt
Find proteins for G0S612 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 50
MoleculeChainsLengthOrganismImage
35S rRNABB [auth C1]2352Chaetomium thermophilum
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Entity ID: 51
MoleculeChainsLengthOrganismImage
U3 snoRNACB [auth C2]230Chaetomium thermophilum
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

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PB [auth CI]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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OB [auth UX]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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QB [auth CI]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references