ISDA

Deposition Date 2019-06-10

Release Date 2019-08-14

Last Version Date 2024-05-22

Entry Detail

PDB ID:

6RXZ

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Chaetomium thermophilum (Taxon ID: 209285)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:35S ribosomal RNA
Chain IDs:AB (auth: C1)
Chain Length:2323
Number of Molecules:1
Biological Source:Chaetomium thermophilum

Polymer Type:polyribonucleotide
Molecule:U3 snoRNA
Chain IDs:BB (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:Putative nucleolar protein
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:127
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:190
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:1163
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:143
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SDL4 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative U3 small nucleolar ribonucleoprotein
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:Putative U3 small nucleolar ribonucleoprotein protein
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:252
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:ZA (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:DB (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:Ribosome biogenesis protein ENP2
Gene (Uniprot):ENP2
Chain IDs:EB (auth: CW)
Chain Length:668
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S902 Pfam ID:PF08159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Enp1
Gene (Uniprot):CTHT_0033170
Chain IDs:KB (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:U3 small nucleolar ribonucleoprotein protein lcp5-like protein
Gene (Uniprot):CTHT_0037520
Chain IDs:LB (auth: CY)
Chain Length:381
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S7Z2 Pfam ID:PF04000

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bfr2
Gene (Uniprot):CTHT_0042520
Chain IDs:MB (auth: CZ)
Chain Length:609
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SAJ6 Pfam ID:PF13339, PF08164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):CTHT_0012920
Chain IDs:LA (auth: Cb)
Chain Length:264
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S1A6 Pfam ID:PF08071, PF00900, PF00467, PF16121

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s5-like protein
Gene (Uniprot):CTHT_0015350
Chain IDs:MA (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 S6
Gene (Uniprot):CTHT_0005340
Chain IDs:NA (auth: Cd)
Chain Length:582
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RY43 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):CTHT_0021240
Chain IDs:OA (auth: Ce)
Chain Length:127
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S8C4 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):CTHT_0005360
Chain IDs:PA (auth: Cf)
Chain Length:202
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RY45 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s9-like protein
Gene (Uniprot):CTHT_0011770
Chain IDs:QA (auth: Cg)
Chain Length:190
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:RA (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:SA (auth: Ci)
Chain Length:1163
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:TA (auth: Cj)
Chain Length:143
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SBR7 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-like protein
Gene (Uniprot):CTHT_0060290
Chain IDs:UA (auth: Ck)
Chain Length:297
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SF00 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Rps18
Gene (Uniprot):CTHT_0026460
Chain IDs:JB (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:VA (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:WA (auth: Cn)
Chain Length:252
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RY17 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):CTHT_0041970.2
Chain IDs:XA (auth: Co)
Chain Length:136
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:P0CU28 Pfam ID:PF01282

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-like protein
Gene (Uniprot):CTHT_0046470
Chain IDs:YA (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:PB (auth: Cz)
Chain Length:609
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:HB (auth: UE), NB (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:GB (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:OB (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:IB (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:Utp20
Gene (Uniprot):CTHT_0072880
Chain IDs:FB (auth: UT)
Chain Length:2612
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SHP3 Pfam ID:PF07539, PF20416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative U3 snoRNP protein
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:CB (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

Primary Citation

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.Show

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