6RXY image
Deposition Date 2019-06-10
Release Date 2019-08-14
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6RXY
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a
Biological Source:
Source Organism:
Chaetomium thermophilum (Taxon ID: 209285)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6RXY validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:35S rRNA
Chain IDs:VA (auth: C1)
Chain Length:2323
Number of Molecules:1
Biological Source:Chaetomium thermophilum
Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:WA (auth: C2)
Chain Length:230
Number of Molecules:1
Biological Source:Chaetomium thermophilum
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop1
Gene (Uniprot):CTHT_0067980
Chain IDs:R (auth: CA), S (auth: CB)
Chain Length:313
Number of Molecules:2
Biological Source:Chaetomium thermophilum
UniProt ID:G0SGY2 Pfam ID:PF01269
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop56
Gene (Uniprot):CTHT_0018510
Chain IDs:T (auth: CC)
Chain Length:212
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S2U4 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nop58
Gene (Uniprot):CTHT_0006520
Chain IDs:U (auth: CD)
Chain Length:582
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RYF6 Pfam ID:PF08156, PF01798
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Snu13
Gene (Uniprot):CTHT_0066810
Chain IDs:V (auth: CE), W (auth: CF)
Chain Length:203
Number of Molecules:2
Biological Source:Chaetomium thermophilum
UniProt ID:G0SGM0 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrp9
Gene (Uniprot):CTHT_0065050
Chain IDs:X (auth: CG)
Chain Length:630
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SG51 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyclase-like protein
Gene (Uniprot):CTHT_0009390
Chain IDs:Y (auth: CH)
Chain Length:151
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S0B1 Pfam ID:PF01137, PF05189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bms1
Gene (Uniprot):CTHT_0030650
Chain IDs:Z (auth: CI)
Chain Length:150
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S445 Pfam ID:PF08142, PF04950
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Imp3
Gene (Uniprot):CTHT_0052200
Chain IDs:AA (auth: CJ)
Chain Length:183
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SDL4 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Imp4
Gene (Uniprot):CTHT_0062900
Chain IDs:BA (auth: CK)
Chain Length:297
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SE90 Pfam ID:PF04427
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mpp10
Gene (Uniprot):CTHT_0046030
Chain IDs:CA (auth: CL)
Chain Length:156
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S9I7 Pfam ID:PF04006
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sof1
Gene (Uniprot):CTHT_0005890
Chain IDs:DA (auth: CM)
Chain Length:446
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RY94 Pfam ID:PF00400, PF04158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Emg1
Gene (Uniprot):CTHT_0048280
Chain IDs:EA (auth: CN), FA (auth: CO)
Chain Length:145
Number of Molecules:2
Biological Source:Chaetomium thermophilum
UniProt ID:G0SAY9 Pfam ID:PF03587
Protein Blast
Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome component
Gene (Uniprot):CTHT_0039040
Chain IDs:GA (auth: CP)
Chain Length:68
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S3V7 Pfam ID:PF17903, PF21800
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein PNO1
Gene (Uniprot):PNO1
Chain IDs:HA (auth: CQ)
Chain Length:259
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S3T2 Pfam ID:PF22891
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Kre33
Gene (Uniprot):NAT10
Chain IDs:IA (auth: CR), JA (auth: CS)
Chain Length:1073
Number of Molecules:2
Biological Source:Chaetomium thermophilum
UniProt ID:G0S273 Pfam ID:PF08351, PF05127, PF13718, PF13725
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Fcf2
Gene (Uniprot):CTHT_0022510
Chain IDs:KA (auth: CT)
Chain Length:203
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S4E3 Pfam ID:PF08698
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Faf1
Gene (Uniprot):CTHT_0024580
Chain IDs:UA (auth: CU)
Chain Length:311
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S5F1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrp7
Gene (Uniprot):CTHT_0051220
Chain IDs:YA (auth: CV)
Chain Length:322
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SDB8 Pfam ID:PF17799, PF12923
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Enp1
Gene (Uniprot):CTHT_0033170
Chain IDs:DB (auth: CX)
Chain Length:480
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S5J4 Pfam ID:PF05291
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s5-like protein
Gene (Uniprot):CTHT_0015350
Chain IDs:LA (auth: Cc)
Chain Length:212
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S1Z0 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):CTHT_0021240
Chain IDs:MA (auth: Ce)
Chain Length:203
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S8C4 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s9-like protein
Gene (Uniprot):CTHT_0011770
Chain IDs:NA (auth: Cg)
Chain Length:630
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S0Z4 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13-like protein
Gene (Uniprot):CTHT_0003530
Chain IDs:OA (auth: Ch)
Chain Length:151
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RZM9 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-like protein
Gene (Uniprot):CTHT_0071230
Chain IDs:PA (auth: Ci)
Chain Length:150
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SFL1 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-like protein
Gene (Uniprot):CTHT_0054540
Chain IDs:QA (auth: Cj)
Chain Length:183
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SBR7 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rps18
Gene (Uniprot):CTHT_0026460
Chain IDs:CB (auth: Cl)
Chain Length:156
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S6J7 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-like protein
Gene (Uniprot):CTHT_0070090
Chain IDs:RA (auth: Cm)
Chain Length:446
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SHI0 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s23-like protein
Gene (Uniprot):CTHT_0005070
Chain IDs:SA (auth: Cn)
Chain Length:145
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RY17 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-like protein
Gene (Uniprot):CTHT_0046470
Chain IDs:TA (auth: Cp)
Chain Length:68
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S9M9 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Rrp5
Gene (Uniprot):CTHT_0026810
Chain IDs:GB (auth: Cz)
Chain Length:1796
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S6T5 Pfam ID:PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2-like protein
Gene (Uniprot):CTHT_0061240
Chain IDs:A (auth: UA)
Chain Length:904
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SF93 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp2
Gene (Uniprot):CTHT_0053180
Chain IDs:B (auth: UB)
Chain Length:907
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SDW0 Pfam ID:PF04147
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp3
Gene (Uniprot):CTHT_0022820
Chain IDs:C (auth: UC)
Chain Length:648
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S4H3 Pfam ID:PF04000, PF09368
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp4
Gene (Uniprot):CTHT_0058380
Chain IDs:D (auth: UD)
Chain Length:884
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SCT7 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp5
Gene (Uniprot):CTHT_0000890
Chain IDs:AB (auth: UE), EB (auth: UI)
Chain Length:410
Number of Molecules:2
Biological Source:Chaetomium thermophilum
UniProt ID:G0RYX2 Pfam ID:PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp6
Gene (Uniprot):CTHT_0020090
Chain IDs:E (auth: UF)
Chain Length:414
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S387 Pfam ID:PF08640
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp7
Gene (Uniprot):CTHT_0002210
Chain IDs:F (auth: UG)
Chain Length:558
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RZ99 Pfam ID:PF00400, PF08149
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp8
Gene (Uniprot):CTHT_0071780
Chain IDs:ZA (auth: UH)
Chain Length:930
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:P0CT47
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp10
Gene (Uniprot):CTHT_0024640
Chain IDs:G (auth: UJ)
Chain Length:1802
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S5L1 Pfam ID:PF12397, PF08146
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 11
Gene (Uniprot):UTP11
Chain IDs:H (auth: UK)
Chain Length:270
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SF32 Pfam ID:PF03998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp12
Gene (Uniprot):CTHT_0003430
Chain IDs:I (auth: UL)
Chain Length:962
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RZL9 Pfam ID:PF00400, PF04003
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp13
Gene (Uniprot):CTHT_0065530
Chain IDs:J (auth: UM)
Chain Length:912
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SG95 Pfam ID:PF00400, PF08625
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp14
Gene (Uniprot):CTHT_0043870
Chain IDs:K (auth: UN)
Chain Length:938
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S8Y4 Pfam ID:PF04615
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp15
Gene (Uniprot):CTHT_0063870
Chain IDs:L (auth: UO)
Chain Length:557
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SEI5 Pfam ID:PF00400, PF09384
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp16
Gene (Uniprot):CTHT_0025640
Chain IDs:FB (auth: UP)
Chain Length:364
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S612 Pfam ID:PF08297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp17
Gene (Uniprot):CTHT_0058290
Chain IDs:M (auth: UQ)
Chain Length:960
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SCS8 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp18
Gene (Uniprot):CTHT_0054250
Chain IDs:N (auth: UR)
Chain Length:618
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0SBN9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Noc4
Gene (Uniprot):CTHT_0003370
Chain IDs:BB (auth: US)
Chain Length:549
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0RZL4 Pfam ID:PF03914
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp21
Gene (Uniprot):CTHT_0037800
Chain IDs:O (auth: UU)
Chain Length:1049
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S872 Pfam ID:PF00400, PF04192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associated protein 22
Gene (Uniprot):CTHT_0016900
Chain IDs:XA (auth: UV)
Chain Length:1171
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S2E0 Pfam ID:PF03813, PF17403, PF17404, PF17405, PF17406, PF17407
Polymer Type:polypeptide(L)
Molecule:Utp24
Chain IDs:P (auth: UX)
Chain Length:193
Number of Molecules:1
Biological Source:Chaetomium thermophilum
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Utp30
Gene (Uniprot):CTHT_0037280
Chain IDs:Q (auth: UZ)
Chain Length:391
Number of Molecules:1
Biological Source:Chaetomium thermophilum
UniProt ID:G0S7X0 Pfam ID:PF00687
Ligand Molecules
ZN
Primary Citation
Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration.
Mol.Cell 75 1256 1269.e7 (2019)
PMID: 31378463 DOI: 10.1016/j.molcel.2019.06.032

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6RXY