› 5oql

Electron Microscopy
3.2Å resolution

Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum

Released:
DOI: 10.2210/pdb5oql/pdb
PDB entry 5oql coloured by chain, front view.
PDB entry 5oql coloured by chain, side view.
PDB entry 5oql coloured by chain, top view.
Source organism: Thermochaetoides thermophila DSM 1495
Primary publication:
3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage.
Cheng J, Kellner N, Berninghausen O, Hurt E, Beckmann R
Nat Struct Mol Biol 24 954-964 (2017)
PMID: 28967883
Related structures: EMD-3847

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-123888 (preferred)
Entry contents:
49 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (51 distinct):
Small-subunit processome Utp12 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 904 amino acids
Theoretical weight: 100.82 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SF93 (Residues: 1-904; Coverage: 100%)
Gene name: CTHT_0061240
Sequence domains:
Nucleolar complex protein 14 Chain: B
Molecule details ›
Chain: B
Length: 907 amino acids
Theoretical weight: 103.96 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SDW0 (Residues: 1-907; Coverage: 100%)
Gene name: CTHT_0053180
Sequence domains: Nop14-like family
Sas10 C-terminal domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 648 amino acids
Theoretical weight: 73.21 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4H3 (Residues: 1-648; Coverage: 100%)
Gene name: CTHT_0022820
Sequence domains:
Utp4 Chain: D
Molecule details ›
Chain: D
Length: 884 amino acids
Theoretical weight: 97.7 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCT7 (Residues: 1-884; Coverage: 100%)
Gene name: CTHT_0058380
Sequence domains: WD domain, G-beta repeat
U3 snoRNP protein Chain: E
Molecule details ›
Chain: E
Length: 414 amino acids
Theoretical weight: 46.92 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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: F
Molecule details ›
Chain: F
Length: 558 amino acids
Theoretical weight: 63.63 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RZ99 (Residues: 1-558; Coverage: 100%)
Gene name: CTHT_0002210
Sequence domains:
U3 small nucleolar RNA-associated protein 10 Chain: G
Molecule details ›
Chain: G
Length: 1802 amino acids
Theoretical weight: 198.51 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S5L1 (Residues: 1-1802; Coverage: 100%)
Gene name: CTHT_0024640
Sequence domains:
U3 small nucleolar RNA-associated protein 11 Chain: H
Molecule details ›
Chain: H
Length: 270 amino acids
Theoretical weight: 31.38 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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: I
Molecule details ›
Chain: I
Length: 962 amino acids
Theoretical weight: 107.57 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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: J
Molecule details ›
Chain: J
Length: 912 amino acids
Theoretical weight: 100.43 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SG95 (Residues: 1-912; Coverage: 100%)
Gene name: CTHT_0065530
Sequence domains:
Utp14 Chain: K
Molecule details ›
Chain: K
Length: 938 amino acids
Theoretical weight: 104.74 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S8Y4 (Residues: 1-938; Coverage: 100%)
Gene name: CTHT_0043870
Sequence domains: Utp14 protein
U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 557 amino acids
Theoretical weight: 60.52 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEI5 (Residues: 1-557; Coverage: 100%)
Gene name: CTHT_0063870
Sequence domains:
Utp17 Chain: M
Molecule details ›
Chain: M
Length: 960 amino acids
Theoretical weight: 105.04 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCS8 (Residues: 1-960; Coverage: 100%)
Gene name: CTHT_0058290
Sequence domains: WD domain, G-beta repeat
Utp18 Chain: N
Molecule details ›
Chain: N
Length: 618 amino acids
Theoretical weight: 69.06 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SBN9 (Residues: 1-618; Coverage: 100%)
Gene name: CTHT_0054250
Small-subunit processome Utp21 domain-containing protein Chain: O
Molecule details ›
Chain: O
Length: 1049 amino acids
Theoretical weight: 115.12 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S872 (Residues: 1-1049; Coverage: 100%)
Gene name: CTHT_0037800
Sequence domains:
PIN domain-containing protein Chain: P
Molecule details ›
Chain: P
Length: 194 amino acids
Theoretical weight: 22.27 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SE30 (Residues: 3-184; Coverage: 99%)
Gene name: CTHT_0062220
Sequence domains: Fcf1
Utp30 Chain: Q
Molecule details ›
Chain: Q
Length: 391 amino acids
Theoretical weight: 43.7 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S7X0 (Residues: 1-391; Coverage: 100%)
Gene name: CTHT_0037280
Sequence domains: Ribosomal protein L1p/L10e family
rRNA 2'-O-methyltransferase fibrillarin Chains: R, S
Molecule details ›
Chains: R, S
Length: 313 amino acids
Theoretical weight: 32.96 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SGY2 (Residues: 1-313; Coverage: 100%)
Gene name: CTHT_0067980
Sequence domains: Fibrillarin
Nucleolar protein 56 Chain: T
Molecule details ›
Chain: T
Length: 523 amino acids
Theoretical weight: 57.83 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S2U4 (Residues: 1-523; Coverage: 100%)
Gene name: CTHT_0018510
Sequence domains:
Nucleolar protein 58 Chain: U
Molecule details ›
Chain: U
Length: 582 amino acids
Theoretical weight: 64.29 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RYF6 (Residues: 1-582; Coverage: 100%)
Gene name: CTHT_0006520
Sequence domains:
13 kDa ribonucleoprotein-associated protein Chains: V, W
Molecule details ›
Chains: V, W
Length: 127 amino acids
Theoretical weight: 13.83 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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: X
Molecule details ›
Chain: X
Length: 630 amino acids
Theoretical weight: 69.61 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SG51 (Residues: 1-630; Coverage: 100%)
Gene name: CTHT_0065050
Sequence domains: WD domain, G-beta repeat
RNA 3'-terminal phosphate cyclase-like protein Chain: Y
Molecule details ›
Chain: Y
Length: 411 amino acids
Theoretical weight: 43.4 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0B1 (Residues: 1-411; Coverage: 100%)
Gene name: CTHT_0009390
Sequence domains:
Bms1-type G domain-containing protein Chain: Z
Molecule details ›
Chain: Z
Length: 1163 amino acids
Theoretical weight: 134.17 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S445 (Residues: 1-1163; Coverage: 100%)
Gene name: CTHT_0030650
Sequence domains:
Imp3 Chain: a
Molecule details ›
Chain: a
Length: 183 amino acids
Theoretical weight: 21.8 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SDL4 (Residues: 1-183; Coverage: 100%)
Gene name: CTHT_0052200
Sequence domains:
U3 small nucleolar ribonucleoprotein protein IMP4 Chain: b
Molecule details ›
Chain: b
Length: 297 amino acids
Theoretical weight: 34.22 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SE90 (Residues: 1-297; Coverage: 100%)
Gene name: CTHT_0062900
Sequence domains: Brix domain
Putative U3 small nucleolar ribonucleoprotein protein Chain: c
Molecule details ›
Chain: c
Length: 785 amino acids
Theoretical weight: 86.08 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S9I7 (Residues: 1-785; Coverage: 100%)
Gene name: CTHT_0046030
Sequence domains: Mpp10 protein
DDB1- and CUL4-associated factor 13 Chain: d
Molecule details ›
Chain: d
Length: 446 amino acids
Theoretical weight: 50.87 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RY94 (Residues: 1-446; Coverage: 100%)
Gene name: CTHT_0005890
Sequence domains:
Nucleolar essential protein 1 Chains: e, f
Molecule details ›
Chains: e, f
Length: 252 amino acids
Theoretical weight: 27.94 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SAY9 (Residues: 1-252; Coverage: 100%)
Gene name: CTHT_0048280
Sequence domains: EMG1/NEP1 methyltransferase
KRR1 small subunit processome component Chain: g
Molecule details ›
Chain: g
Length: 322 amino acids
Theoretical weight: 37.5 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S3V7 (Residues: 1-322; Coverage: 100%)
Gene name: CTHT_0039040
Sequence domains:
Pre-rRNA-processing protein PNO1 Chain: h
Molecule details ›
Chain: h
Length: 259 amino acids
Theoretical weight: 28.72 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S3T2 (Residues: 1-259; Coverage: 100%)
Gene names: CTHT_0030540, DIM2, PNO1
RNA cytidine acetyltransferase Chains: i, j
Molecule details ›
Chains: i, j
Length: 1073 amino acids
Theoretical weight: 119.8 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S273 (Residues: 1-1073; Coverage: 100%)
Gene names: CTHT_0016220, NAT10
Sequence domains:
Fcf2 pre-rRNA processing C-terminal domain-containing protein Chain: k
Molecule details ›
Chain: k
Length: 203 amino acids
Theoretical weight: 22.57 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4E3 (Residues: 1-203; Coverage: 100%)
Gene name: CTHT_0022510
Sequence domains: Fcf2 pre-rRNA processing
Small ribosomal subunit protein eS1 Chain: l
Molecule details ›
Chain: l
Length: 255 amino acids
Theoretical weight: 29.25 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S7T8 (Residues: 1-255; Coverage: 100%)
Gene names: CTHT_0028780, RPS1
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein S4 Chain: m
Molecule details ›
Chain: m
Length: 264 amino acids
Theoretical weight: 29.8 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S1A6 (Residues: 1-264; Coverage: 100%)
Gene name: CTHT_0012920
Sequence domains:
Small ribosomal subunit protein uS7 domain-containing protein Chain: n
Molecule details ›
Chain: n
Length: 212 amino acids
Theoretical weight: 23.68 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S1Z0 (Residues: 1-212; Coverage: 100%)
Gene name: CTHT_0015350
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S6 Chain: o
Molecule details ›
Chain: o
Length: 239 amino acids
Theoretical weight: 27.49 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RY43 (Residues: 1-239; Coverage: 100%)
Gene name: CTHT_0005340
Sequence domains: Ribosomal protein S6e
40S ribosomal protein S7 Chain: p
Molecule details ›
Chain: p
Length: 203 amino acids
Theoretical weight: 23.08 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S8C4 (Residues: 1-203; Coverage: 100%)
Gene name: CTHT_0021240
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S8 Chain: q
Molecule details ›
Chain: q
Length: 202 amino acids
Theoretical weight: 23.1 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RY45 (Residues: 1-202; Coverage: 100%)
Gene name: CTHT_0005360
Sequence domains: Ribosomal protein S8e
40S ribosomal protein s9-like protein Chain: r
Molecule details ›
Chain: r
Length: 190 amino acids
Theoretical weight: 22.03 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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: s
Molecule details ›
Chain: s
Length: 151 amino acids
Theoretical weight: 16.91 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RZM9 (Residues: 1-151; Coverage: 100%)
Gene name: CTHT_0003530
Sequence domains:
40S ribosomal protein S14-like protein Chain: t
Molecule details ›
Chain: t
Length: 150 amino acids
Theoretical weight: 16.07 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SFL1 (Residues: 1-150; Coverage: 100%)
Gene name: CTHT_0071230
Sequence domains: Ribosomal protein S11
40S ribosomal protein S16-like protein Chain: u
Molecule details ›
Chain: u
Length: 143 amino acids
Theoretical weight: 15.96 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SBR7 (Residues: 1-143; Coverage: 100%)
Gene name: CTHT_0054540
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: v
Molecule details ›
Chain: v
Length: 161 amino acids
Theoretical weight: 18.7 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SF00 (Residues: 1-161; Coverage: 100%)
Gene name: CTHT_0060290
Sequence domains:
40S ribosomal protein S22-like protein Chain: w
Molecule details ›
Chain: w
Length: 130 amino acids
Theoretical weight: 14.91 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SHI0 (Residues: 1-130; Coverage: 100%)
Gene name: CTHT_0070090
Sequence domains: Ribosomal protein S8
40S ribosomal protein s23-like protein Chain: x
Molecule details ›
Chain: x
Length: 145 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RY17 (Residues: 1-145; Coverage: 100%)
Gene name: CTHT_0005070
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein eS24 Chain: y
Molecule details ›
Chain: y
Length: 136 amino acids
Theoretical weight: 15.54 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: P0CU28 (Residues: 1-136; Coverage: 100%)
Gene name: CTHT_0041970.2
Sequence domains: Ribosomal protein S24e
40S ribosomal protein S28-like protein Chain: z
Molecule details ›
Chain: z
Length: 68 amino acids
Theoretical weight: 7.74 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S9M9 (Residues: 1-68; Coverage: 100%)
Gene name: CTHT_0046470
Sequence domains: Ribosomal protein S28e
Faf1 Chain: 0
Molecule details ›
Chain: 0
Length: 311 amino acids
Theoretical weight: 34.58 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S5F1 (Residues: 1-311; Coverage: 100%)
Gene name: CTHT_0024580
35S rRNA Chain: 1
Molecule details ›
Chain: 1
Length: 2568 nucleotides
Theoretical weight: 827.8 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA
U3 snoRNA Chain: 2
Molecule details ›
Chain: 2
Length: 274 nucleotides
Theoretical weight: 87.99 KDa
Sequence domains: Fungal small nucleolar RNA U3

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-3847

Quick links

Citations

17 review citations

Eukaryotic Ribosome Assembly.
Baßler et al. (2019)
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2 mentions without citation

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Farrell et al. (2020)
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