6RXY

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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 --: --

  • DOI: 10.1016/j.molcel.2019.06.032
  • Primary Citation of Related Structures:  

  • 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 stepwi ...

    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.,Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.,Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany. Electronic address: beckmann@genzentrum.lmu.de.,Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany. Electronic address: ed.hurt@bzh.uni-heidelberg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periodic tryptophan protein 2-like protein
UA
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
UB
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
UC
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
UD
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
UF
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
UG
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
UJ
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
UK
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
UL
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
UM
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
UN
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
UO
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
UQ
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
UR
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
Utp21
UU
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
UX
193N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Utp30
UZ
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
CA, CB
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
Nop56
CC
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
CD
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
CE, CF
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
CG
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
CH
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
CI
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
CJ
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
Imp4
CK
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
Mpp10
CL
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
CM
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
CN, CO
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
CP
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
CQ
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
Kre33
CR, CS
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
CT
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 s5-like protein
Cc
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: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
Ce
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: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein s9-like protein
Cg
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: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13-like protein
Ch
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: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-like protein
Ci
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: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-like protein
Cj
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: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-like protein
Cm
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: 41
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein s23-like protein
Cn
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: 42
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-like protein
Cp
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: 43
MoleculeChainsSequence LengthOrganismDetails
Faf1
CU
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: 46
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 22
UV
1171Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S2E0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S2E0
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Rrp7
CV
322Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SDB8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SDB8
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Utp8
UH
930Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for P0CT47 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  P0CT47
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Utp5
UE, UI
410Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RYX2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYX2
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Noc4
US
549Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RZL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RZL4
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Rps18
Cl
156Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S6J7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S6J7
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Enp1
CX
480Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S5J4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S5J4
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Utp16
UP
364Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S612 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S612
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Rrp5
Cz
1796Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S6T5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S6T5
Entity ID: 44
MoleculeChainsLengthOrganism
35S rRNAC12323Chaetomium thermophilum
Entity ID: 45
MoleculeChainsLengthOrganism
U3 snoRNAC2230Chaetomium thermophilum
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.7 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: 2019-08-14
    Type: Initial release