› 6rxx

Electron Microscopy
7.1Å resolution

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

Released:
DOI: 10.2210/pdb6rxx/pdb
PDB entry 6rxx coloured by chain, front view.
PDB entry 6rxx coloured by chain, side view.
PDB entry 6rxx coloured by chain, top view.
Source organism: Thermochaetoides thermophila
Primary publication:
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
Mol Cell 75 1256-1269.e7 (2019)
PMID: 31378463
Related structures: EMD-10054

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 68-mer (preferred)
PDBe Complex ID:
PDB-CPX-123884 (preferred)
Entry contents:
61 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (63 distinct):
Small-subunit processome Utp12 domain-containing protein Chain: UA
Molecule details ›
Chain: UA
Length: 904 amino acids
Theoretical weight: 100.82 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SF93 (Residues: 1-904; Coverage: 100%)
Gene name: CTHT_0061240
Sequence domains:
Sas10 C-terminal domain-containing protein Chain: UC
Molecule details ›
Chain: UC
Length: 648 amino acids
Theoretical weight: 73.21 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S4H3 (Residues: 1-648; Coverage: 100%)
Gene name: CTHT_0022820
Sequence domains:
U3 snoRNP protein Chain: UF
Molecule details ›
Chain: UF
Length: 414 amino acids
Theoretical weight: 46.92 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S387 (Residues: 1-414; Coverage: 100%)
Gene name: CTHT_0020090
Sequence domains: U3 small nucleolar RNA-associated protein 6
BING4 C-terminal domain-containing protein Chain: UG
Molecule details ›
Chain: UG
Length: 558 amino acids
Theoretical weight: 63.63 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RZ99 (Residues: 1-558; Coverage: 100%)
Gene name: CTHT_0002210
Sequence domains:
U3 small nucleolar RNA-associated protein 11 Chain: UK
Molecule details ›
Chain: UK
Length: 270 amino acids
Theoretical weight: 31.38 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SF32 (Residues: 1-270; Coverage: 100%)
Gene names: CTHT_0060630, UTP11
Sequence domains: Utp11 protein
Small-subunit processome Utp12 domain-containing protein Chain: UL
Molecule details ›
Chain: UL
Length: 962 amino acids
Theoretical weight: 107.57 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RZL9 (Residues: 1-962; Coverage: 100%)
Gene name: CTHT_0003430
Sequence domains:
U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing protein Chain: UM
Molecule details ›
Chain: UM
Length: 912 amino acids
Theoretical weight: 100.43 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SG95 (Residues: 1-912; Coverage: 100%)
Gene name: CTHT_0065530
Sequence domains:
Utp14 Chain: UN
Molecule details ›
Chain: UN
Length: 938 amino acids
Theoretical weight: 104.74 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S8Y4 (Residues: 1-938; Coverage: 100%)
Gene name: CTHT_0043870
Sequence domains: Utp14 protein
Utp18 Chain: UR
Molecule details ›
Chain: UR
Length: 618 amino acids
Theoretical weight: 69.06 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SBN9 (Residues: 1-618; Coverage: 100%)
Gene name: CTHT_0054250
Small-subunit processome Utp21 domain-containing protein Chain: UU
Molecule details ›
Chain: UU
Length: 1049 amino acids
Theoretical weight: 115.12 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S872 (Residues: 1-1049; Coverage: 100%)
Gene name: CTHT_0037800
Sequence domains:
Utp24 Chain: UX
Molecule details ›
Chain: UX
Length: 193 amino acids
Theoretical weight: 22.14 KDa
Source organism: Thermochaetoides thermophila
Imp3 Chain: CJ
Molecule details ›
Chain: CJ
Length: 183 amino acids
Theoretical weight: 21.8 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SDL4 (Residues: 1-183; Coverage: 100%)
Gene name: CTHT_0052200
Sequence domains:
U3 small nucleolar ribonucleoprotein protein IMP4 Chain: CK
Molecule details ›
Chain: CK
Length: 297 amino acids
Theoretical weight: 34.22 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SE90 (Residues: 1-297; Coverage: 100%)
Gene name: CTHT_0062900
Sequence domains: Brix domain
Putative U3 small nucleolar ribonucleoprotein protein Chain: CL
Molecule details ›
Chain: CL
Length: 785 amino acids
Theoretical weight: 86.08 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S9I7 (Residues: 1-785; Coverage: 100%)
Gene name: CTHT_0046030
Sequence domains: Mpp10 protein
DDB1- and CUL4-associated factor 13 Chain: CM
Molecule details ›
Chain: CM
Length: 446 amino acids
Theoretical weight: 50.87 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RY94 (Residues: 1-446; Coverage: 100%)
Gene name: CTHT_0005890
Sequence domains:
Nucleolar essential protein 1 Chains: CN, CO
Molecule details ›
Chains: CN, CO
Length: 252 amino acids
Theoretical weight: 27.94 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SAY9 (Residues: 1-252; Coverage: 100%)
Gene name: CTHT_0048280
Sequence domains: EMG1/NEP1 methyltransferase
KRR1 small subunit processome component Chain: CP
Molecule details ›
Chain: CP
Length: 322 amino acids
Theoretical weight: 37.5 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S3V7 (Residues: 1-322; Coverage: 100%)
Gene name: CTHT_0039040
Sequence domains:
Pre-rRNA-processing protein PNO1 Chain: CQ
Molecule details ›
Chain: CQ
Length: 259 amino acids
Theoretical weight: 28.72 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S3T2 (Residues: 1-259; Coverage: 100%)
Gene names: CTHT_0030540, DIM2, PNO1
Small ribosomal subunit protein eS1 Chain: Ca
Molecule details ›
Chain: Ca
Length: 255 amino acids
Theoretical weight: 29.25 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S7T8 (Residues: 1-255; Coverage: 100%)
Gene names: CTHT_0028780, RPS1
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS7 domain-containing protein Chain: Cc
Molecule details ›
Chain: Cc
Length: 212 amino acids
Theoretical weight: 23.68 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S1Z0 (Residues: 1-212; Coverage: 100%)
Gene name: CTHT_0015350
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S7 Chain: Ce
Molecule details ›
Chain: Ce
Length: 203 amino acids
Theoretical weight: 23.08 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S8C4 (Residues: 1-203; Coverage: 100%)
Gene name: CTHT_0021240
Sequence domains: Ribosomal protein S7e
40S ribosomal protein s9-like protein Chain: Cg
Molecule details ›
Chain: Cg
Length: 190 amino acids
Theoretical weight: 22.03 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S0Z4 (Residues: 1-190; Coverage: 100%)
Gene name: CTHT_0011770
Sequence domains:
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: Ch
Molecule details ›
Chain: Ch
Length: 151 amino acids
Theoretical weight: 16.91 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RZM9 (Residues: 1-151; Coverage: 100%)
Gene name: CTHT_0003530
Sequence domains:
40S ribosomal protein S14-like protein Chain: Ci
Molecule details ›
Chain: Ci
Length: 150 amino acids
Theoretical weight: 16.07 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SFL1 (Residues: 1-150; Coverage: 100%)
Gene name: CTHT_0071230
Sequence domains: Ribosomal protein S11
40S ribosomal protein S16-like protein Chain: Cj
Molecule details ›
Chain: Cj
Length: 143 amino acids
Theoretical weight: 15.96 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SBR7 (Residues: 1-143; Coverage: 100%)
Gene name: CTHT_0054540
Sequence domains: Ribosomal protein S9/S16
40S ribosomal protein S22-like protein Chain: Cm
Molecule details ›
Chain: Cm
Length: 130 amino acids
Theoretical weight: 14.91 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SHI0 (Residues: 1-130; Coverage: 100%)
Gene name: CTHT_0070090
Sequence domains: Ribosomal protein S8
40S ribosomal protein s23-like protein Chain: Cn
Molecule details ›
Chain: Cn
Length: 145 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RY17 (Residues: 1-145; Coverage: 100%)
Gene name: CTHT_0005070
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S28-like protein Chain: Cp
Molecule details ›
Chain: Cp
Length: 68 amino acids
Theoretical weight: 7.74 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S9M9 (Residues: 1-68; Coverage: 100%)
Gene name: CTHT_0046470
Sequence domains: Ribosomal protein S28e
Ribosomal protein s27-like protein Chain: Cq
Molecule details ›
Chain: Cq
Length: 82 amino acids
Theoretical weight: 8.92 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S1S4 (Residues: 1-82; Coverage: 100%)
Gene name: CTHT_0014630
Sequence domains: Ribosomal protein S27
Faf1 Chain: CU
Molecule details ›
Chain: CU
Length: 311 amino acids
Theoretical weight: 34.58 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S5F1 (Residues: 1-311; Coverage: 100%)
Gene name: CTHT_0024580
U3 small nucleolar RNA-associated protein 22 Chain: UV
Molecule details ›
Chain: UV
Length: 1171 amino acids
Theoretical weight: 131.11 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S2E0 (Residues: 1-1171; Coverage: 100%)
Gene name: CTHT_0016900
Sequence domains:
Rrp7 Chain: CV
Molecule details ›
Chain: CV
Length: 322 amino acids
Theoretical weight: 36.37 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SDB8 (Residues: 1-322; Coverage: 100%)
Gene name: CTHT_0051220
Sequence domains:
Putative ribosomal protein Chain: Cl
Molecule details ›
Chain: Cl
Length: 156 amino acids
Theoretical weight: 17.83 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S6J7 (Residues: 1-156; Coverage: 100%)
Gene name: CTHT_0026460
Sequence domains: Ribosomal protein S13/S18
RNA 3'-terminal phosphate cyclase-like protein Chain: CH
Molecule details ›
Chain: CH
Length: 411 amino acids
Theoretical weight: 43.4 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S0B1 (Residues: 1-411; Coverage: 100%)
Gene name: CTHT_0009390
Sequence domains:
Bms1-type G domain-containing protein Chain: CI
Molecule details ›
Chain: CI
Length: 1163 amino acids
Theoretical weight: 134.17 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S445 (Residues: 1-1163; Coverage: 100%)
Gene name: CTHT_0030650
Sequence domains:
RNA cytidine acetyltransferase Chains: CR, CS
Molecule details ›
Chains: CR, CS
Length: 1073 amino acids
Theoretical weight: 119.8 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S273 (Residues: 1-1073; Coverage: 100%)
Gene names: CTHT_0016220, NAT10
Sequence domains:
40S ribosomal protein S4 Chain: Cb
Molecule details ›
Chain: Cb
Length: 264 amino acids
Theoretical weight: 29.8 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S1A6 (Residues: 1-264; Coverage: 100%)
Gene name: CTHT_0012920
Sequence domains:
40S ribosomal protein S6 Chain: Cd
Molecule details ›
Chain: Cd
Length: 239 amino acids
Theoretical weight: 27.49 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RY43 (Residues: 1-239; Coverage: 100%)
Gene name: CTHT_0005340
Sequence domains: Ribosomal protein S6e
40S ribosomal protein S8 Chain: Cf
Molecule details ›
Chain: Cf
Length: 202 amino acids
Theoretical weight: 23.1 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RY45 (Residues: 1-202; Coverage: 100%)
Gene name: CTHT_0005360
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: Ck
Molecule details ›
Chain: Ck
Length: 161 amino acids
Theoretical weight: 18.7 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SF00 (Residues: 1-161; Coverage: 100%)
Gene name: CTHT_0060290
Sequence domains:
Small ribosomal subunit protein eS24 Chain: Co
Molecule details ›
Chain: Co
Length: 136 amino acids
Theoretical weight: 15.54 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: P0CU28 (Residues: 1-136; Coverage: 100%)
Gene name: CTHT_0041970.2
Sequence domains: Ribosomal protein S24e
Ribosome biogenesis protein ENP2 Chain: CW
Molecule details ›
Chain: CW
Length: 668 amino acids
Theoretical weight: 75.83 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S902 (Residues: 1-668; Coverage: 100%)
Gene names: CTHT_0044060, ENP2
Sequence domains: NUC153 domain
Utp20 Chain: UT
Molecule details ›
Chain: UT
Length: 2612 amino acids
Theoretical weight: 295.28 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SHP3 (Residues: 1-2612; Coverage: 100%)
Gene name: CTHT_0072880
Sequence domains:
Protein BFR2 Chain: CZ
Molecule details ›
Chain: CZ
Length: 609 amino acids
Theoretical weight: 69.04 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SAJ6 (Residues: 1-609; Coverage: 100%)
Gene name: CTHT_0042520
Sequence domains:
Nucleolar complex protein 14 Chain: UB
Molecule details ›
Chain: UB
Length: 907 amino acids
Theoretical weight: 103.96 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SDW0 (Residues: 1-907; Coverage: 100%)
Gene name: CTHT_0053180
Sequence domains: Nop14-like family
Utp4 Chain: UD
Molecule details ›
Chain: UD
Length: 884 amino acids
Theoretical weight: 97.7 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SCT7 (Residues: 1-884; Coverage: 100%)
Gene name: CTHT_0058380
Sequence domains: WD domain, G-beta repeat
U3 small nucleolar RNA-associated protein 10 Chain: UJ
Molecule details ›
Chain: UJ
Length: 1802 amino acids
Theoretical weight: 198.51 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S5L1 (Residues: 1-1802; Coverage: 100%)
Gene name: CTHT_0024640
Sequence domains:
U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing protein Chain: UO
Molecule details ›
Chain: UO
Length: 557 amino acids
Theoretical weight: 60.52 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SEI5 (Residues: 1-557; Coverage: 100%)
Gene name: CTHT_0063870
Sequence domains:
Utp17 Chain: UQ
Molecule details ›
Chain: UQ
Length: 960 amino acids
Theoretical weight: 105.04 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SCS8 (Residues: 1-960; Coverage: 100%)
Gene name: CTHT_0058290
Sequence domains: WD domain, G-beta repeat
Bystin-like protein Chain: CX
Molecule details ›
Chain: CX
Length: 480 amino acids
Theoretical weight: 54.32 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S5J4 (Residues: 1-480; Coverage: 100%)
Gene name: CTHT_0033170
Sequence domains: Bystin
Small-subunit processome Utp12 domain-containing protein Chains: UE, UI
Molecule details ›
Chains: UE, UI
Length: 410 amino acids
Theoretical weight: 44.66 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RYX2 (Residues: 1-410; Coverage: 100%)
Gene name: CTHT_0000890
Sequence domains: Dip2/Utp12 Family
Utp16 Chain: UP
Molecule details ›
Chain: UP
Length: 364 amino acids
Theoretical weight: 40.73 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S612 (Residues: 1-364; Coverage: 100%)
Gene name: CTHT_0025640
Sequence domains: U3 snoRNA associated
Utp8 Chain: UH
Molecule details ›
Chain: UH
Length: 930 amino acids
Theoretical weight: 102.42 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: P0CT47 (Residues: 1-930; Coverage: 100%)
Gene name: CTHT_0071780
CCAAT-binding factor domain-containing protein Chain: US
Molecule details ›
Chain: US
Length: 549 amino acids
Theoretical weight: 63.33 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RZL4 (Residues: 1-549; Coverage: 100%)
Gene name: CTHT_0003370
Sequence domains: CBF/Mak21 family
rRNA 2'-O-methyltransferase fibrillarin Chains: CA, CB
Molecule details ›
Chains: CA, CB
Length: 313 amino acids
Theoretical weight: 32.96 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SGY2 (Residues: 1-313; Coverage: 100%)
Gene name: CTHT_0067980
Sequence domains: Fibrillarin
Nucleolar protein 56 Chain: CC
Molecule details ›
Chain: CC
Length: 523 amino acids
Theoretical weight: 57.83 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S2U4 (Residues: 1-523; Coverage: 100%)
Gene name: CTHT_0018510
Sequence domains:
Nucleolar protein 58 Chain: CD
Molecule details ›
Chain: CD
Length: 582 amino acids
Theoretical weight: 64.29 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0RYF6 (Residues: 1-582; Coverage: 100%)
Gene name: CTHT_0006520
Sequence domains:
13 kDa ribonucleoprotein-associated protein Chains: CE, CF
Molecule details ›
Chains: CE, CF
Length: 127 amino acids
Theoretical weight: 13.83 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SGM0 (Residues: 1-127; Coverage: 100%)
Gene name: CTHT_0066810
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal RNA-processing protein Chain: CG
Molecule details ›
Chain: CG
Length: 630 amino acids
Theoretical weight: 69.61 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SG51 (Residues: 1-630; Coverage: 100%)
Gene name: CTHT_0065050
Sequence domains: WD domain, G-beta repeat
Fcf2 pre-rRNA processing C-terminal domain-containing protein Chain: CT
Molecule details ›
Chain: CT
Length: 203 amino acids
Theoretical weight: 22.57 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0S4E3 (Residues: 1-203; Coverage: 100%)
Gene name: CTHT_0022510
Sequence domains: Fcf2 pre-rRNA processing
40S ribosomal protein S19-like protein Chain: Cr
Molecule details ›
Chain: Cr
Length: 153 amino acids
Theoretical weight: 17.15 KDa
Source organism: Thermochaetoides thermophila
UniProt:
  • Canonical: G0SFK8 (Residues: 1-153; Coverage: 100%)
Gene name: CTHT_0071200
Sequence domains: Ribosomal protein S19e
35S ribosomal RNA Chain: C1
Molecule details ›
Chain: C1
Length: 1859 nucleotides
Theoretical weight: 599.29 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
U3 snoRNA Chain: C2
Molecule details ›
Chain: C2
Length: 232 nucleotides
Theoretical weight: 74.58 KDa
Sequence domains: Fungal small nucleolar RNA U3

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.1Å
Relevant EMDB volumes: EMD-10054

Quick links

Citations

8 review citations

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
7 more