› 8i9r

Electron Microscopy
3.1Å resolution

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP

Released:
DOI: 10.2210/pdb8i9r/pdb
PDB entry 8i9r coloured by chain, front view.
PDB entry 8i9r coloured by chain, side view.
PDB entry 8i9r 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-35281

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 49-mer (preferred)
PDBe Complex ID:
PDB-CPX-215715 (preferred)
Entry contents:
45 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (48 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:
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:
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:
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
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
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
Ribosomal RNA-processing protein 15 Chain: Ch
Molecule details ›
Chain: Ch
Length: 354 amino acids
Theoretical weight: 38.31 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S5P7 (Residues: 1-354; Coverage: 100%)
Gene name: CTHT_0025020
Sequence domains: Rrp15p
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
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
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 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
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 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
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
Ribosomal RNA-processing protein 1 Chain: Cc
Molecule details ›
Chain: Cc
Length: 282 amino acids
Theoretical weight: 32.13 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4M2 (Residues: 1-282; Coverage: 100%)
Gene name: CTHT_0031510
Sequence domains: Nucleolar protein,Nop52
Brix domain-containing protein Chain: Cd
Molecule details ›
Chain: Cd
Length: 436 amino acids
Theoretical weight: 49.47 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4S2 (Residues: 1-436; Coverage: 100%)
Gene name: CTHT_0023330
Sequence domains: Brix domain
Protein MAK16 Chain: Ce
Molecule details ›
Chain: Ce
Length: 336 amino acids
Theoretical weight: 39.46 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SFD6 (Residues: 1-336; Coverage: 100%)
Gene name: CTHT_0061670
Sequence domains:
60S ribosome biogenesis protein Rrp14 Chain: Cf
Molecule details ›
Chain: Cf
Length: 570 amino acids
Theoretical weight: 64.47 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S2I7 (Residues: 1-570; Coverage: 100%)
Gene name: CTHT_0017370
Sequence domains:
Ribosome production factor 2 homolog Chain: Cy
Molecule details ›
Chain: Cy
Length: 350 amino acids
Theoretical weight: 39.93 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SF80 (Residues: 1-350; Coverage: 100%)
Gene name: CTHT_0061110
Sequence domains: Brix domain
Brix domain-containing protein Chain: Cg
Molecule details ›
Chain: Cg
Length: 478 amino acids
Theoretical weight: 54.25 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S732 (Residues: 1-478; Coverage: 100%)
Gene name: CTHT_0035970
Sequence domains: Brix domain
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:
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:
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
Ribosome biogenesis regulatory protein Chain: Cx
Molecule details ›
Chain: Cx
Length: 202 amino acids
Theoretical weight: 22.82 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SCH6 (Residues: 1-202; Coverage: 100%)
Gene name: CTHT_0057260
Sequence domains: Ribosome biogenesis regulatory protein (RRS1)
Putative ribosomal protein Chain: LJ
Molecule details ›
Chain: LJ
Length: 173 amino acids
Theoretical weight: 20.12 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SHQ2 (Residues: 1-173; Coverage: 100%)
Gene name: CTHT_0072970
Sequence domains:
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: LD
Molecule details ›
Chain: LD
Length: 304 amino acids
Theoretical weight: 35.03 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEG2 (Residues: 1-304; Coverage: 100%)
Gene name: CTHT_0063640
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
RNA (3341-MER) Chain: C1
Molecule details ›
Chain: C1
Length: 3341 nucleotides
Theoretical weight: 1080.02 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
RNA (256-MER) Chain: C2
Molecule details ›
Chain: C2
Length: 256 nucleotides
Theoretical weight: 82.47 KDa
Sequence domains: 5.8S ribosomal RNA
RNA (119-MER) Chain: C4
Molecule details ›
Chain: C4
Length: 119 nucleotides
Theoretical weight: 38.31 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
1 modified residue:
Ligand OMU 3 x OMU

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-35281

Quick links

Citations

3 citation in other articles

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