› 8i9z

Electron Microscopy
2.7Å resolution

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4

Released:
DOI: 10.2210/pdb8i9z/pdb
PDB entry 8i9z coloured by chain, front view.
PDB entry 8i9z coloured by chain, side view.
PDB entry 8i9z coloured by chain, top view.
Source organism: Thermochaetoides thermophila DSM 1495
Primary publication:
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
EMBO Rep e56910 (2023)
PMID: 37129998
Related structures: EMD-35289

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Dolichyl diphosphooligosaccharide + [protein]-L-asparagine = dolichyl diphosphate + a glycoprotein with the oligosaccharide chain attached by N-beta-D-glycosyl linkage to a protein L-asparagine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 60-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215709 (preferred)
Entry contents:
57 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (59 distinct):
Brix domain-containing protein Chain: CA
Molecule details ›
Chain: CA
Length: 316 amino acids
Theoretical weight: 36.48 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RXZ3 (Residues: 1-316; Coverage: 100%)
Gene name: CTHT_0004820
Sequence domains: Brix domain
Ribosome biogenesis protein C8F11.04 Chain: CB
Molecule details ›
Chain: CB
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
Ribosome biogenesis protein ERB1 Chain: CC
Molecule details ›
Chain: CC
Length: 801 amino acids
Theoretical weight: 90.84 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCK6 (Residues: 1-801; Coverage: 100%)
Gene names: CTHT_0057570, ERB1
Sequence domains:
Ribosome biogenesis protein YTM1 Chain: CD
Molecule details ›
Chain: CD
Length: 495 amino acids
Theoretical weight: 52.99 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SFB5 (Residues: 1-495; Coverage: 100%)
Gene names: CTHT_0061460, YTM1
Sequence domains:
ATP-dependent RNA helicase Chain: CE
Molecule details ›
Chain: CE
Length: 598 amino acids
Theoretical weight: 66.83 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RYU9 (Residues: 1-542, 543-556; Coverage: 100%)
Gene name: CTHT_0000650
Sequence domains:
Large ribosomal subunit protein uL10 Chain: CF
Molecule details ›
Chain: CF
Length: 270 amino acids
Theoretical weight: 30.55 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S616 (Residues: 1-270; Coverage: 100%)
Gene name: CTHT_0025680
Sequence domains:
60S ribosome subunit biogenesis protein NIP7 Chain: CG
Molecule details ›
Chain: CG
Length: 184 amino acids
Theoretical weight: 20.69 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S435 (Residues: 1-184; Coverage: 100%)
Gene name: CTHT_0022410
Sequence domains:
Nucleolar GTP-binding protein 1 Chain: CH
Molecule details ›
Chain: CH
Length: 661 amino acids
Theoretical weight: 75.62 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S8F1 (Residues: 1-661; Coverage: 100%)
Gene names: CTHT_0029660, NOG1
Sequence domains:
RRM domain-containing protein Chain: CI
Molecule details ›
Chain: CI
Length: 414 amino acids
Theoretical weight: 45.88 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S1H0 (Residues: 1-414; Coverage: 100%)
Gene name: CTHT_0013570
Sequence domains: RNA recognition motif
Pescadillo homolog Chain: CJ
Molecule details ›
Chain: CJ
Length: 679 amino acids
Theoretical weight: 77.17 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SHX6 (Residues: 1-679; Coverage: 100%)
Gene names: CTHT_0073720, NOP7
Sequence domains:
Ribosome biogenesis protein NSA2 homolog Chain: CK
Molecule details ›
Chain: CK
Length: 261 amino acids
Theoretical weight: 29.72 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S081 (Residues: 1-261; Coverage: 100%)
Gene name: CTHT_0009080
Sequence domains: Ribosomal protein S8e
CP-type G domain-containing protein Chain: CL
Molecule details ›
Chain: CL
Length: 558 amino acids
Theoretical weight: 61.52 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEW3 (Residues: 1-558; Coverage: 100%)
Gene name: CTHT_0059920
Sequence domains:
60S ribosomal protein l7-like protein Chains: CM, LF
Molecule details ›
Chains: CM, LF
Length: 249 amino acids
Theoretical weight: 28.82 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SFL0 (Residues: 1-249; Coverage: 100%)
Gene name: CTHT_0071220
Sequence domains:
Eukaryotic translation initiation factor 6 Chain: CN
Molecule details ›
Chain: CN
Length: 246 amino acids
Theoretical weight: 26.47 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S683 (Residues: 1-246; Coverage: 100%)
Gene names: CTHT_0025830, TIF6
Sequence domains: eIF-6 family
DUF2423 domain-containing protein Chain: CO
Molecule details ›
Chain: CO
Length: 120 amino acids
Theoretical weight: 13.26 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SHK0 (Residues: 1-120; Coverage: 100%)
Gene name: CTHT_0070290
Sequence domains: Protein of unknown function (DUF2423)
SAM-dependent MTase RsmB/NOP-type domain-containing protein Chain: CP
Molecule details ›
Chain: CP
Length: 751 amino acids
Theoretical weight: 83.66 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SHQ0 (Residues: 1-751; Coverage: 100%)
Gene name: CTHT_0072950
Sequence domains:
Ribosome biogenesis protein RLP24 Chain: CQ
Molecule details ›
Chain: CQ
Length: 225 amino acids
Theoretical weight: 26.43 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S497 (Residues: 1-225; Coverage: 100%)
Gene name: CTHT_0039400
Sequence domains: Ribosomal protein L24e
Nucleolar protein 16 Chain: CR
Molecule details ›
Chain: CR
Length: 237 amino acids
Theoretical weight: 26.96 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S832 (Residues: 1-237; Coverage: 100%)
Gene name: CTHT_0029200
Sequence domains: Ribosome biogenesis protein Nop16
AdoMet-dependent rRNA methyltransferase SPB1 Chain: CS
Molecule details ›
Chain: CS
Length: 834 amino acids
Theoretical weight: 95.51 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SGD8 (Residues: 1-834; Coverage: 100%)
Gene name: CTHT_0065960
Sequence domains:
Nucleolar complex-associated protein 3 Chain: CT
Molecule details ›
Chain: CT
Length: 688 amino acids
Theoretical weight: 77.95 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S5L0 (Residues: 1-688; Coverage: 100%)
Gene name: CTHT_0024630
Sequence domains:
rRNA processing protein Chain: CU
Molecule details ›
Chain: CU
Length: 451 amino acids
Theoretical weight: 50.26 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SGC2 (Residues: 1-451; Coverage: 100%)
Gene name: CTHT_0065800
Sequence domains: Eukaryotic rRNA processing protein EBP2
Large ribosomal subunit protein eL28 Chain: CV
Molecule details ›
Chain: CV
Length: 147 amino acids
Theoretical weight: 15.96 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SHJ6 (Residues: 1-147; Coverage: 100%)
Gene name: CTHT_0070250
Sequence domains: Ribosomal L28e protein family
ATP-dependent RNA helicase Chain: CW
Molecule details ›
Chain: CW
Length: 679 amino acids
Theoretical weight: 75.47 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RYG4 (Residues: 1-679; Coverage: 100%)
Gene name: CTHT_0006600
Sequence domains:
60S ribosomal subunit-like protein Chain: CX
Molecule details ›
Chain: CX
Length: 203 amino acids
Theoretical weight: 22.68 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SGJ0 (Residues: 1-203; Coverage: 100%)
Gene name: CTHT_0066500
Putative NOC2 family protein Chain: CY
Molecule details ›
Chain: CY
Length: 788 amino acids
Theoretical weight: 89.77 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SD05 (Residues: 1-788; Coverage: 100%)
Gene name: CTHT_0059020
Sequence domains: Noc2p family
rRNA-processing protein Chain: Cz
Molecule details ›
Chain: Cz
Length: 123 amino acids
Theoretical weight: 14.71 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCP3 (Residues: 1-123; Coverage: 100%)
Gene name: CTHT_0057940
Sequence domains: Cgr1 family
60S ribosomal protein L3-like protein Chain: LB
Molecule details ›
Chain: LB
Length: 392 amino acids
Theoretical weight: 44.46 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RXW1 (Residues: 1-392; Coverage: 100%)
Gene name: CTHT_0004490
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 C-terminal domain-containing protein Chain: LC
Molecule details ›
Chain: LC
Length: 365 amino acids
Theoretical weight: 39.44 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SFC3 (Residues: 1-365; Coverage: 100%)
Gene name: CTHT_0061540
Sequence domains:
60S ribosomal protein L6 Chain: LE
Molecule details ›
Chain: LE
Length: 200 amino acids
Theoretical weight: 22.13 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0D6 (Residues: 1-200; Coverage: 100%)
Gene name: CTHT_0009640
Sequence domains: Ribosomal protein L6e
60S ribosomal protein L8 Chain: LG
Molecule details ›
Chain: LG
Length: 262 amino acids
Theoretical weight: 29.74 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SAJ9 (Residues: 1-262; Coverage: 100%)
Gene name: CTHT_0042550
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6 alpha-beta domain-containing protein Chain: LH
Molecule details ›
Chain: LH
Length: 192 amino acids
Theoretical weight: 21.58 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0E5 (Residues: 1-229; Coverage: 84%)
Gene name: CTHT_0009740
Sequence domains: Ribosomal protein L6
60S ribosomal protein L12-like protein Chain: LK
Molecule details ›
Chain: LK
Length: 165 amino acids
Theoretical weight: 17.8 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SGH8 (Residues: 1-165; Coverage: 100%)
Gene name: CTHT_0066380
Sequence domains:
60S ribosomal protein L13 Chain: LL
Molecule details ›
Chain: LL
Length: 213 amino acids
Theoretical weight: 24.19 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S992 (Residues: 1-213; Coverage: 100%)
Gene name: CTHT_0045000
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 domain-containing protein Chain: LM
Molecule details ›
Chain: LM
Length: 142 amino acids
Theoretical weight: 16.11 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S1R0 (Residues: 1-142; Coverage: 100%)
Gene name: CTHT_0014490
Sequence domains: Ribosomal protein L14
Ribosomal protein L15 Chain: LN
Molecule details ›
Chain: LN
Length: 203 amino acids
Theoretical weight: 24.31 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RZ88 (Residues: 1-203; Coverage: 100%)
Gene name: CTHT_0002100
Sequence domains: Ribosomal L15
60S ribosomal protein L16-like protein Chain: LO
Molecule details ›
Chain: LO
Length: 204 amino acids
Theoretical weight: 22.99 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SH61 (Residues: 1-204; Coverage: 100%)
Gene name: CTHT_0068840
Sequence domains: Ribosomal protein L13
60S ribosomal protein l17-like protein Chain: LP
Molecule details ›
Chain: LP
Length: 187 amino acids
Theoretical weight: 21.07 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SGY1 (Residues: 1-187; Coverage: 100%)
Gene name: CTHT_0067970
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: LQ
Molecule details ›
Chain: LQ
Length: 213 amino acids
Theoretical weight: 24.2 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S9B5 (Residues: 1-213; Coverage: 100%)
Gene name: CTHT_0045230
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Ribosomal protein L19 Chain: LR
Molecule details ›
Chain: LR
Length: 2898 amino acids
Theoretical weight: 317.09 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S9T3 (Residues: 1-2898; Coverage: 100%)
Gene name: CTHT_0047080
Sequence domains:
60S ribosomal protein L20 Chain: LS
Molecule details ›
Chain: LS
Length: 174 amino acids
Theoretical weight: 20.34 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCE2 (Residues: 1-174; Coverage: 100%)
Gene name: CTHT_0056900
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
60S ribosomal protein l21-like protein Chain: LT
Molecule details ›
Chain: LT
Length: 160 amino acids
Theoretical weight: 18.16 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0Z3 (Residues: 1-160; Coverage: 100%)
Gene name: CTHT_0011760
Sequence domains: Ribosomal protein L21e
60S ribosomal protein L22-like protein Chain: LU
Molecule details ›
Chain: LU
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SDS8 (Residues: 1-127; Coverage: 100%)
Gene name: CTHT_0052850
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein l23-like protein Chain: LV
Molecule details ›
Chain: LV
Length: 139 amino acids
Theoretical weight: 14.67 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SI44 (Residues: 1-139; Coverage: 100%)
Gene name: CTHT_0074440
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL23 N-terminal domain-containing protein Chain: LX
Molecule details ›
Chain: LX
Length: 156 amino acids
Theoretical weight: 17.18 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S507 (Residues: 1-156; Coverage: 100%)
Gene name: CTHT_0023650
Sequence domains:
KOW domain-containing protein Chain: LY
Molecule details ›
Chain: LY
Length: 138 amino acids
Theoretical weight: 15.57 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RYN9 (Residues: 1-138; Coverage: 100%)
Gene name: CTHT_0007360
Sequence domains:
60S ribosomal protein L27 Chain: LZ
Molecule details ›
Chain: LZ
Length: 135 amino acids
Theoretical weight: 15.8 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0RZE9 (Residues: 1-135; Coverage: 100%)
Gene name: CTHT_0002720
Sequence domains: Ribosomal L27e protein family
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: Lc
Molecule details ›
Chain: Lc
Length: 108 amino acids
Theoretical weight: 11.6 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEI0 (Residues: 1-108; Coverage: 100%)
Gene name: CTHT_0063820
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Putative 60S ribosomal protein Chain: Ld
Molecule details ›
Chain: Ld
Length: 120 amino acids
Theoretical weight: 13.87 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SD68 (Residues: 1-120; Coverage: 100%)
Gene name: CTHT_0059140
Sequence domains: Ribosomal protein L31e
60S ribosomal protein L32-like protein Chain: Le
Molecule details ›
Chain: Le
Length: 131 amino acids
Theoretical weight: 15.1 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S6V4 (Residues: 1-131; Coverage: 100%)
Gene name: CTHT_0027000
Sequence domains: Ribosomal protein L32
60S ribosomal protein l33-like protein Chain: Lf
Molecule details ›
Chain: Lf
Length: 109 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCL3 (Residues: 1-109; Coverage: 100%)
Gene name: CTHT_0057640
Sequence domains: Ribosomal protein L35Ae
Ribosomal protein l34-like protein Chain: Lg
Molecule details ›
Chain: Lg
Length: 119 amino acids
Theoretical weight: 13.49 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SFN0 (Residues: 1-119; Coverage: 100%)
Gene name: CTHT_0071430
Sequence domains: Ribosomal protein L34e
dolichyl-diphosphooligosaccharide--protein glycotransferase Chain: Lh
Molecule details ›
Chain: Lh
Length: 935 amino acids
Theoretical weight: 105.17 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S0D7 (Residues: 1-935; Coverage: 100%)
Gene name: CTHT_0009650
Sequence domains:
60S ribosomal protein L36 Chain: Li
Molecule details ›
Chain: Li
Length: 110 amino acids
Theoretical weight: 12.78 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SBN1 (Residues: 1-110; Coverage: 100%)
Gene name: CTHT_0054170
Sequence domains: Ribosomal protein L36e
Ribosomal protein L37 Chain: Lj
Molecule details ›
Chain: Lj
Length: 95 amino acids
Theoretical weight: 10.66 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S101 (Residues: 1-95; Coverage: 100%)
Gene name: CTHT_0011850
Sequence domains: Ribosomal protein L37e
60S ribosomal protein L38-like protein Chain: Lk
Molecule details ›
Chain: Lk
Length: 81 amino acids
Theoretical weight: 9.52 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SG89 (Residues: 1-94; Coverage: 86%)
Gene name: CTHT_0065470
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: Ll
Molecule details ›
Chain: Ll
Length: 51 amino acids
Theoretical weight: 6.3 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: Q2H9R2 (Residues: 1-51; Coverage: 100%)
Gene name: CHGG_03042
Sequence domains: Ribosomal L39 protein
Ribosomal protein Chain: Lq
Molecule details ›
Chain: Lq
Length: 217 amino acids
Theoretical weight: 24.06 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4Z9 (Residues: 1-217; Coverage: 100%)
Gene name: CTHT_0023560
Sequence domains: Ribosomal protein L1p/L10e family
RNA (3341-MER) Chain: C1
Molecule details ›
Chain: C1
Length: 3341 nucleotides
Theoretical weight: 1079.98 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
RNA (319-MER) Chain: C2
Molecule details ›
Chain: C2
Length: 319 nucleotides
Theoretical weight: 102.61 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand GTP 1 x GTP
Ligand ZN 2 x ZN
Ligand ADP 1 x ADP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-35289

Quick links

Citations

2 citation in other articles

Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
Lau et al. (2023)
1 more

1 mention without citation

Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Thoms et al. (2023)