6RXZ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 proteinUA904Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SF93 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Utp2UB907Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SDW0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Utp3UC648Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S4H3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Utp4UD884Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SCT7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Utp6UF414Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S387 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Utp7UG558Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RZ99 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UTP10UJ1802Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S5L1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11UK270Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SF32 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Utp12UL962Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RZL9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Utp13UM912Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SG95 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Utp14UN938Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S8Y4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Utp15UO557Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SEI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Utp17UQ960Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SCS8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Utp18UR618Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SBN9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 snoRNP proteinUU1049Chaetomium thermophilumMutation(s): 0 
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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Utp24UX193Chaetomium thermophilumMutation(s): 0 
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Entity ID: 17
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Utp30UZ391Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S7X0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Nop1CACB313Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SGY2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Putative nucleolar proteinCC523Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S2U4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Nop58CD582Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RYF6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Snu13CECF127Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SGM0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Rrp9CG630Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SG51 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinCH411Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S0B1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Bms1CI1163Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S445 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Imp3CJ183Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SDL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoproteinCK297Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SE90 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoprotein proteinCL785Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S9I7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Sof1CM446Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RY94 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Emg1CNCO252Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SAY9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
KRR1 small subunit processome componentCP322Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S3V7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1CQ259Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S3T2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Kre33CRCS1073Chaetomium thermophilumMutation(s): 0 
EC: 2.3.1
Find proteins for G0S273 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Fcf2CT203Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S4E3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4Cb264Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S1A6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinCc212Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S1Z0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6Cd239Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RY43 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7Ce203Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S8C4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8Cf202Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RY45 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinCg190Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S0Z4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinCh151Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RZM9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinCi150Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SFL1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinCj143Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SBR7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinCk161Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SF00 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinCm130Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SHI0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 45
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40S ribosomal protein s23-like proteinCn145Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RY17 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 46
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40S ribosomal protein S24Co136Chaetomium thermophilumMutation(s): 0 
Find proteins for P0CU28 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 47
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40S ribosomal protein S28-like proteinCp68Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S9M9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Faf1CU311Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S5F1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 51
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U3 small nucleolar RNA-associated protein 22UV1171Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S2E0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 52
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Rrp7CV322Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SDB8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2CW668Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S902 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Utp20UT2612Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SHP3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Utp8UH930Chaetomium thermophilumMutation(s): 0 
Find proteins for P0CT47 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Utp5UEUI410Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RYX2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
Noc4US549Chaetomium thermophilumMutation(s): 0 
Find proteins for G0RZL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 58
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Rps18Cl156Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S6J7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 59
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Enp1CX480Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S5J4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 60
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U3 small nucleolar ribonucleoprotein protein lcp5-like proteinCY381Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S7Z2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Bfr2CZ609Chaetomium thermophilumMutation(s): 0 
Find proteins for G0SAJ6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Utp16UP364Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S612 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 63
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Rrp5Cz1796Chaetomium thermophilumMutation(s): 0 
Find proteins for G0S6T5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 49
MoleculeChainsLengthOrganismImage
35S ribosomal RNAC12323Chaetomium thermophilum
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Entity ID: 50
MoleculeChainsLengthOrganismImage
U3 snoRNAC2230Chaetomium thermophilum
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references