ISDA: 9XAF

Deposition Date 2025-10-22

Release Date 2026-06-24

Last Version Date 2026-06-24

Entry Detail

PDB ID:

9XAF

Keywords:

RIBOSOME

Title:

Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state a

Biological Source:

Source Organism(s):

Thermochaetoides thermophila (Taxon ID: 209285)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:35s rna
Chain IDs:VA (auth: C1)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

Polymer Type:polyribonucleotide
Molecule:u3 rna
Chain IDs:WA (auth: C2)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:rRNA 2'-O-methyltransferase f
Gene (Uniprot):CTHT_0067980
Chain IDs:R (auth: CA), S (auth: CB)
Chain Length:0
Number of Molecules:2
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SGY2 Pfam ID:PF01269

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 56
Gene (Uniprot):CTHT_0018510
Chain IDs:T (auth: CC)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S2U4 Pfam ID:PF08156, PF01798

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar protein 58
Gene (Uniprot):CTHT_0006520
Chain IDs:U (auth: CD)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RYF6 Pfam ID:PF08156, PF01798

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:H/ACA ribonucleoprotein compl
Gene (Uniprot):CTHT_0066810
Chain IDs:V (auth: CE), W (auth: CF)
Chain Length:0
Number of Molecules:2
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SGM0 Pfam ID:PF01248

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal RNA-processing prot
Gene (Uniprot):CTHT_0065050
Chain IDs:X (auth: CG)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SG51 Pfam ID:PF00400

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA 3'-terminal phosphate cyc
Gene (Uniprot):CTHT_0009390
Chain IDs:Y (auth: CH)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S0B1 Pfam ID:PF01137, PF05189

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bms1-type G domain-containing
Gene (Uniprot):CTHT_0030650
Chain IDs:Z (auth: CI)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S445 Pfam ID:PF01926, PF08142, PF04950

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleo
Gene (Uniprot):CTHT_0052200
Chain IDs:AA (auth: CJ)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SDL4 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleo
Gene (Uniprot):CTHT_0062900
Chain IDs:BA (auth: CK)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SE90 Pfam ID:PF04427

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative U3 small nucleolar r
Gene (Uniprot):CTHT_0046030
Chain IDs:CA (auth: CL)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S9I7 Pfam ID:PF04006

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:DDB1- and CUL4-associated fac
Gene (Uniprot):CTHT_0005890
Chain IDs:DA (auth: CM)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RY94 Pfam ID:PF00400, PF04158

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar essential protein 1
Gene (Uniprot):CTHT_0048280
Chain IDs:EA (auth: CN), FA (auth: CO)
Chain Length:0
Number of Molecules:2
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SAY9 Pfam ID:PF03587

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:KRR1 small subunit processome
Gene (Uniprot):CTHT_0039040
Chain IDs:GA (auth: CP)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S3V7 Pfam ID:PF17903, PF21800

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pre-rRNA-processing protein P
Gene (Uniprot):PNO1
Chain IDs:HA (auth: CQ)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S3T2 Pfam ID:PF22891

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA cytidine acetyltransferas
Gene (Uniprot):NAT10
Chain IDs:IA (auth: CR), JA (auth: CS)
Chain Length:0
Number of Molecules:2
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S273 Pfam ID:PF08351, PF05127, PF13718, PF13725 EC:2.3.1.-

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Fcf2 pre-rRNA processing C-te
Gene (Uniprot):CTHT_0022510
Chain IDs:KA (auth: CT)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S4E3 Pfam ID:PF08698

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:faf1
Gene (Uniprot):CTHT_0024580
Chain IDs:UA (auth: CU)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S5F1

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bystin-like protein
Gene (Uniprot):CTHT_0033170
Chain IDs:BB (auth: CX)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S5J4 Pfam ID:PF05291

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar ribonucleo
Gene (Uniprot):CTHT_0037520
Chain IDs:CB (auth: CY)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S7Z2 Pfam ID:PF04000

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s5-like
Gene (Uniprot):CTHT_0015350
Chain IDs:LA (auth: Cc)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S1Z0 Pfam ID:PF00177

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):CTHT_0021240
Chain IDs:MA (auth: Ce)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S8C4 Pfam ID:PF01251

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s9-like
Gene (Uniprot):CTHT_0011770
Chain IDs:NA (auth: Cg)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S0Z4 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-lik
Gene (Uniprot):CTHT_0071230
Chain IDs:OA (auth: Ci)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SFL1 Pfam ID:PF00411

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-lik
Gene (Uniprot):CTHT_0054540
Chain IDs:PA (auth: Cj)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SBR7 Pfam ID:PF00380

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative ribosomal protein
Gene (Uniprot):CTHT_0026460
Chain IDs:AB (auth: Cl)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S6J7 Pfam ID:PF00416

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-lik
Gene (Uniprot):CTHT_0070090
Chain IDs:QA (auth: Cm)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SHI0 Pfam ID:PF00410

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein s23-lik
Gene (Uniprot):CTHT_0005070
Chain IDs:RA (auth: Cn)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RY17 Pfam ID:PF00164

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):CTHT_0041970.2
Chain IDs:SA (auth: Co)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:P0CU28 Pfam ID:PF01282

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-lik
Gene (Uniprot):CTHT_0046470
Chain IDs:TA (auth: Cp)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S9M9 Pfam ID:PF01200

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Periodic tryptophan protein 2
Gene (Uniprot):CTHT_0061240
Chain IDs:A (auth: UA)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SF93 Pfam ID:PF00400, PF04003

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nucleolar complex protein 14
Gene (Uniprot):CTHT_0053180
Chain IDs:B (auth: UB)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SDW0 Pfam ID:PF04147

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Sas10 C-terminal domain-conta
Gene (Uniprot):CTHT_0022820
Chain IDs:C (auth: UC)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S4H3 Pfam ID:PF04000, PF09368

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:UTP4
Gene (Uniprot):CTHT_0058380
Chain IDs:D (auth: UD)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SCT7 Pfam ID:PF00400

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small-subunit processome Utp1
Gene (Uniprot):CTHT_0000890
Chain IDs:YA (auth: UE), DB (auth: UI)
Chain Length:0
Number of Molecules:2
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RYX2 Pfam ID:PF04003

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 snoRNP protein
Gene (Uniprot):CTHT_0020090
Chain IDs:E (auth: UF)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S387 Pfam ID:PF08640, PF23233

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U three protein 7
Gene (Uniprot):CTHT_0002210
Chain IDs:F (auth: UG)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RZ99 Pfam ID:PF00400, PF08149

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:utp8
Gene (Uniprot):CTHT_0071780
Chain IDs:XA (auth: UH)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:P0CT47

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):CTHT_0024640
Chain IDs:G (auth: UJ)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S5L1 Pfam ID:PF12397, PF23243, PF08146

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):UTP11
Chain IDs:H (auth: UK)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SF32 Pfam ID:PF03998

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small-subunit processome Utp1
Gene (Uniprot):CTHT_0003430
Chain IDs:I (auth: UL)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RZL9 Pfam ID:PF25173, PF25172, PF04003

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):CTHT_0065530
Chain IDs:J (auth: UM)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SG95 Pfam ID:PF00400, PF08625

Polymer Type:polypeptide(L)
Molecule:UTP14
Chain IDs:K (auth: UN)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:U3 small nucleolar RNA-associ
Gene (Uniprot):CTHT_0063870
Chain IDs:L (auth: UO)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SEI5 Pfam ID:PF00400, PF09384

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:utp16
Gene (Uniprot):CTHT_0025640
Chain IDs:EB (auth: UP)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S612 Pfam ID:PF08297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:UTP17
Gene (Uniprot):CTHT_0058290
Chain IDs:M (auth: UQ)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SCS8 Pfam ID:PF23869

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:UTP18
Gene (Uniprot):CTHT_0054250
Chain IDs:N (auth: UR)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0SBN9

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:CCAAT-binding factor domain-c
Gene (Uniprot):CTHT_0003370
Chain IDs:ZA (auth: US)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0RZL4 Pfam ID:PF03914

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Putative U3 snoRNP protein
Gene (Uniprot):CTHT_0037800
Chain IDs:O (auth: UU)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S872 Pfam ID:PF25171, PF25168, PF04192

Polymer Type:polypeptide(L)
Molecule:UTP24
Chain IDs:P (auth: UX)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein C
Gene (Uniprot):CTHT_0037280
Chain IDs:Q (auth: UZ)
Chain Length:0
Number of Molecules:1
Biological Source:Thermochaetoides thermophila

UniProt ID:G0S7X0 Pfam ID:PF00687

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
SEP	A	SER	modified residue

Ligand Molecules

ADP

GTP

Primary Citation

Nucleoplasmic checkpoint of the 40S ribosomal decoding center maturation.

Lau, B, Li, Y, Zhu, J, Ye, X, Fischer, P, Hong, X, Yuan, R, Beckmann, R, Hurt, E, Cheng, J.Show

Cell Rep 45 117545 117545 (2026)

PMID: 42275223 DOI: 10.1016/j.celrep.2026.117545

Abstact

The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late cytoplasmic steps and their checkpoint mechanisms are well characterized, the regulation of early nucleoplasmic DC assembly is unclear. Here, we show that the essential assembly factor Rrp12 plays a central coordinating role. Using Chaetomium thermophilum and cryo-electron microscopy analyses of fifteen pre-40S intermediates, we demonstrate that Rrp12 C terminus truncation: (1) inhibits release of the Utp14-Dhr1 pair, (2) displaces Tsr1, (3) promotes premature stabilization of h28, and (4) prevents h44 formation. These defects impair final 18S rRNA processing and prematurely activate the quality control kinase Rio1. Our results reveal a nucleoplasmic checkpoint during DC formation and establish Rrp12 as a critical regulator ensuring accurate assembly and orderly ribosome maturation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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