ISDA

Deposition Date 2023-02-07

Release Date 2023-05-17

Last Version Date 2024-11-06

Entry Detail

PDB ID:

8IA0

Keywords:

RIBOSOME

Title:

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6

Biological Source:

Source Organism:

Chaetomium thermophilum (Taxon ID: 759272)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.70 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:RNA (3341-MER)
Chain IDs:A (auth: C1)
Chain Length:3341
Number of Molecules:1
Biological Source:Chaetomium thermophilum

Polymer Type:polyribonucleotide
Molecule:RNA (319-MER)
Chain IDs:B (auth: C2)
Chain Length:319
Number of Molecules:1
Biological Source:Chaetomium thermophilum

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Brix domain-containing protein
Gene (Uniprot):CTHT_0004820
Chain IDs:C (auth: CA)
Chain Length:316
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RXZ3 Pfam ID:PF04427

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein C8F11.04
Gene (Uniprot):CTHT_0037280
Chain IDs:D (auth: CB)
Chain Length:391
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S7X0 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein ERB1
Gene (Uniprot):ERB1
Chain IDs:E (auth: CC)
Chain Length:801
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SCK6 Pfam ID:PF08145, PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein YTM1
Gene (Uniprot):YTM1
Chain IDs:F (auth: CD)
Chain Length:495
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SFB5 Pfam ID:PF08154, PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA helicase
Gene (Uniprot):CTHT_0000650
Chain IDs:G (auth: CE)
Chain Length:598
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RYU9 Pfam ID:PF00270, PF00271, PF13959

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome assembly factor mrt4
Gene (Uniprot):CTHT_0025680
Chain IDs:H (auth: CF)
Chain Length:270
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S616 Pfam ID:PF00466, PF17777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosome subunit biogenesis protein NIP7
Gene (Uniprot):CTHT_0022410
Chain IDs:I (auth: CG)
Chain Length:184
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S435 Pfam ID:PF17833, PF03657

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 1
Gene (Uniprot):NOG1
Chain IDs:J (auth: CH)
Chain Length:661
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S8F1 Pfam ID:PF17835, PF06858, PF08155

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative RNA-binding protein
Gene (Uniprot):CTHT_0013570
Chain IDs:K (auth: CI)
Chain Length:414
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S1H0 Pfam ID:PF00076

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pescadillo homolog
Gene (Uniprot):NOP7
Chain IDs:L (auth: CJ)
Chain Length:679
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SHX6 Pfam ID:PF06732, PF00533

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2 homolog
Gene (Uniprot):CTHT_0009080
Chain IDs:M (auth: CK)
Chain Length:261
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S081 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative GTP binding protein
Gene (Uniprot):CTHT_0059920
Chain IDs:N (auth: CL)
Chain Length:558
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SEW3 Pfam ID:PF08701, PF01926

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l7-like protein
Gene (Uniprot):CTHT_0071220
Chain IDs:O (auth: CM), IA (auth: LF)
Chain Length:249
Number of Molecules:2
Biological Source:Chaetomium thermophilum

UniProt ID:G0SFL0 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):TIF6
Chain IDs:P (auth: CN)
Chain Length:246
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S683 Pfam ID:PF01912

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DUF2423 domain-containing protein
Gene (Uniprot):CTHT_0070290
Chain IDs:Q (auth: CO)
Chain Length:120
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SHK0 Pfam ID:PF10338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA methyltransferase nop2-like protein
Gene (Uniprot):CTHT_0072950
Chain IDs:R (auth: CP)
Chain Length:751
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SHQ0 Pfam ID:PF22458, PF01189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein RLP24
Gene (Uniprot):CTHT_0039400
Chain IDs:S (auth: CQ)
Chain Length:225
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S497 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 16
Gene (Uniprot):CTHT_0029200
Chain IDs:T (auth: CR)
Chain Length:237
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S832 Pfam ID:PF09420

Protein Blast

Polymer Type:polypeptide(L)
Molecule:AdoMet-dependent rRNA methyltransferase SPB1
Gene (Uniprot):CTHT_0065960
Chain IDs:U (auth: CS)
Chain Length:834
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SGD8 Pfam ID:PF01728, PF11861, PF07780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar complex-associated protein 3
Gene (Uniprot):CTHT_0024630
Chain IDs:V (auth: CT)
Chain Length:688
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S5L0 Pfam ID:PF07540, PF03914

Protein Blast

Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein EBP2
Gene (Uniprot):CTHT_0065800
Chain IDs:W (auth: CU)
Chain Length:451
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SGC2 Pfam ID:PF05890

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 60S ribosomal protein
Gene (Uniprot):CTHT_0070250
Chain IDs:X (auth: CV)
Chain Length:147
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SHJ6 Pfam ID:PF01778

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase
Gene (Uniprot):CTHT_0006600
Chain IDs:Y (auth: CW)
Chain Length:679
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RYG4 Pfam ID:PF00270, PF00271, PF13959

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal subunit-like protein
Gene (Uniprot):CTHT_0066500
Chain IDs:Z (auth: CX)
Chain Length:203
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SGJ0

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative NOC2 family protein
Gene (Uniprot):CTHT_0059020
Chain IDs:AA (auth: CY)
Chain Length:788
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SD05 Pfam ID:PF03715

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PUM-HD domain-containing protein
Gene (Uniprot):CTHT_0010150
Chain IDs:BA (auth: CZ)
Chain Length:123
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S0I6 Pfam ID:PF08144

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 12
Gene (Uniprot):CTHT_0027900
Chain IDs:CA (auth: Ca)
Chain Length:316
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S7E9 Pfam ID:PF09805

Protein Blast

Polymer Type:polypeptide(L)
Molecule:rRNA-processing protein
Gene (Uniprot):CTHT_0057940
Chain IDs:DA (auth: Cz)
Chain Length:123
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SCP3 Pfam ID:PF03879

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-like protein
Gene (Uniprot):CTHT_0023090
Chain IDs:EA (auth: LA)
Chain Length:254
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S4P8 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3-like protein
Gene (Uniprot):CTHT_0004490
Chain IDs:FA (auth: LB)
Chain Length:392
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RXW1 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-like protein
Gene (Uniprot):CTHT_0061540
Chain IDs:GA (auth: LC)
Chain Length:365
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SFC3 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):CTHT_0009640
Chain IDs:HA (auth: LE)
Chain Length:200
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S0D6 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8
Gene (Uniprot):CTHT_0042550
Chain IDs:JA (auth: LG)
Chain Length:262
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SAJ9 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l9-like protein
Gene (Uniprot):CTHT_0009740
Chain IDs:KA (auth: LH)
Chain Length:192
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S0E5 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12-like protein
Gene (Uniprot):CTHT_0066380
Chain IDs:LA (auth: LK)
Chain Length:165
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SGH8 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):CTHT_0045000
Chain IDs:MA (auth: LL)
Chain Length:213
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S992 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-like protein
Gene (Uniprot):CTHT_0014490
Chain IDs:NA (auth: LM)
Chain Length:142
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S1R0 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):CTHT_0002100
Chain IDs:OA (auth: LN)
Chain Length:203
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RZ88 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-like protein
Gene (Uniprot):CTHT_0068840
Chain IDs:PA (auth: LO)
Chain Length:204
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SH61 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l17-like protein
Gene (Uniprot):CTHT_0067970
Chain IDs:QA (auth: LP)
Chain Length:92
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SGY1 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L18-like protein
Gene (Uniprot):CTHT_0045230
Chain IDs:RA (auth: LQ)
Chain Length:217
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S9B5 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L19
Gene (Uniprot):CTHT_0047080
Chain IDs:SA (auth: LR)
Chain Length:2898
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S9T3 Pfam ID:PF12074, PF13513, PF21040, PF10274, PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20
Gene (Uniprot):CTHT_0056900
Chain IDs:TA (auth: LS)
Chain Length:174
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SCE2 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l21-like protein
Gene (Uniprot):CTHT_0011760
Chain IDs:UA (auth: LT)
Chain Length:160
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S0Z3 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-like protein
Gene (Uniprot):CTHT_0052850
Chain IDs:VA (auth: LU)
Chain Length:127
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SDS8 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l23-like protein
Gene (Uniprot):CTHT_0074440
Chain IDs:WA (auth: LV)
Chain Length:139
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SI44 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25-like protein
Gene (Uniprot):CTHT_0023650
Chain IDs:XA (auth: LX)
Chain Length:156
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S507 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-like protein
Gene (Uniprot):CTHT_0007360
Chain IDs:YA (auth: LY)
Chain Length:138
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RYN9 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):CTHT_0002720
Chain IDs:ZA (auth: LZ)
Chain Length:135
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0RZE9 Pfam ID:PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l30-like protein
Gene (Uniprot):CTHT_0063820
Chain IDs:AB (auth: Lc)
Chain Length:365
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SEI0 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative 60S ribosomal protein
Gene (Uniprot):CTHT_0059140
Chain IDs:BB (auth: Ld)
Chain Length:120
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SD68 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32-like protein
Gene (Uniprot):CTHT_0027000
Chain IDs:CB (auth: Le)
Chain Length:200
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S6V4 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein l33-like protein
Gene (Uniprot):CTHT_0057640
Chain IDs:DB (auth: Lf)
Chain Length:109
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SCL3 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein l34-like protein
Gene (Uniprot):CTHT_0071430
Chain IDs:EB (auth: Lg)
Chain Length:262
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SFN0 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:dolichyl-diphosphooligosaccharide--protein glycotransferase
Gene (Uniprot):CTHT_0009650
Chain IDs:FB (auth: Lh)
Chain Length:192
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S0D7 Pfam ID:PF00831, PF02516, PF21436

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):CTHT_0054170
Chain IDs:GB (auth: Li)
Chain Length:110
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SBN1 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):CTHT_0011850
Chain IDs:HB (auth: Lj)
Chain Length:95
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S101 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38-like protein
Gene (Uniprot):CTHT_0065470
Chain IDs:IB (auth: Lk)
Chain Length:165
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0SG89 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):CHGG_03042
Chain IDs:KB (auth: Ll)
Chain Length:213
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:Q2H9R2 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-like protein
Gene (Uniprot):CTHT_0026110
Chain IDs:JB (auth: Lp)
Chain Length:92
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S6B0 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):CTHT_0023560
Chain IDs:LB (auth: Lq)
Chain Length:217
Number of Molecules:1
Biological Source:Chaetomium thermophilum

UniProt ID:G0S4Z9 Pfam ID:PF00687

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
SEP	E	SER	modified residue
TPO	E	THR	modified residue

Ligand Molecules

ADP

GTP

Primary Citation

Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.

Lau, B, Huang, Z, Kellner, N, Niu, S, Berninghausen, O, Beckmann, R, Hurt, E, Cheng, J.Show

Embo Rep. 24 e56910 e56910 (2023)

PMID: 37129998 DOI: 10.15252/embr.202356910

Abstact

Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.

Legend

Protein

Chemical

Disease

Primary Citation of related structures