› 8pv8

Electron Microscopy
2.91Å resolution

Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure

Released:
DOI: 10.2210/pdb8pv8/pdb
PDB entry 8pv8 coloured by chain, front view.
PDB entry 8pv8 coloured by chain, side view.
PDB entry 8pv8 coloured by chain, top view.
Source organism: Thermochaetoides thermophila DSM 1495
Primary publication:
Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E
EMBO Rep e57984 (2023)
PMID: 37921038
Related structures: EMD-17957

Function and Biology Details

Reaction catalysed: 
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-238604 (preferred)
Entry contents:
55 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (58 distinct):
Large ribosomal subunit protein uL10 Chain: CF
Molecule details ›
Chain: CF
Length: 270 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S616 (Residues: 1-270; Coverage: 100%)
Gene name: CTHT_0025680
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:
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: 61.48 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SEW3 (Residues: 1-558; Coverage: 100%)
Gene name: CTHT_0059920
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: YBL028C ribosome biogenesis factor, N-terminal domain
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
C2H2-type domain-containing protein Chain: Cb
Molecule details ›
Chain: Cb
Length: 117 amino acids
Theoretical weight: 13.71 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SB32 (Residues: 1-117; Coverage: 100%)
Gene name: CTHT_0048710
Sequence domains: Zinc-finger double-stranded RNA-binding
Nucleolar GTP-binding protein 2 Chain: Cd
Molecule details ›
Chain: Cd
Length: 627 amino acids
Theoretical weight: 70.31 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0SBX1 (Residues: 1-627; Coverage: 100%)
Gene name: CTHT_0055100
Sequence domains:
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
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: LA
Molecule details ›
Chain: LA
Length: 254 amino acids
Theoretical weight: 27.6 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S4P8 (Residues: 1-254; Coverage: 100%)
Gene name: CTHT_0023090
Sequence domains:
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 l7-like protein Chain: LF
Molecule details ›
Chain: 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:
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 l9-like protein Chain: LH
Molecule details ›
Chain: LH
Length: 192 amino acids
Theoretical weight: 21.57 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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 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
60S ribosomal protein L28-like protein Chain: La
Molecule details ›
Chain: La
Length: 149 amino acids
Theoretical weight: 16.85 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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: 9.54 KDa
Source organism: Thermochaetoides thermophila DSM 1495
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
60S ribosomal protein L43-like protein Chain: Lp
Molecule details ›
Chain: Lp
Length: 92 amino acids
Theoretical weight: 10.16 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S6B0 (Residues: 1-92; Coverage: 100%)
Gene name: CTHT_0026110
Sequence domains: Ribosomal L37ae protein family
Pre-rRNA-processing protein IPI3 Chains: CT, CU
Molecule details ›
Chains: CT, CU
Length: 437 amino acids
Theoretical weight: 47.63 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S1T5 (Residues: 1-437; Coverage: 100%)
Gene name: CTHT_0014750
Sequence domains: WD domain, G-beta repeat
Pre-rRNA-processing protein RIX1 Chains: CV, CW
Molecule details ›
Chains: CV, CW
Length: 781 amino acids
Theoretical weight: 84.85 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S5R0 (Residues: 1-781; Coverage: 100%)
Gene name: CTHT_0025150
Sequence domains: rRNA processing/ribosome biogenesis
Pre-rRNA-processing protein IPI1 Chain: CS
Molecule details ›
Chain: CS
Length: 338 amino acids
Theoretical weight: 37.44 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: P0CT45 (Residues: 1-338; Coverage: 100%)
Gene names: CTHT_0115680, IPI1
Sequence domains: Rix1 complex component involved in 60S ribosome maturation
Protein SDA1 Chain: CR
Molecule details ›
Chain: CR
Length: 767 amino acids
Theoretical weight: 86.96 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: G0S215 (Residues: 1-767; Coverage: 100%)
Gene names: CTHT_0015620, SDA1
Sequence domains:
Ribosomal protein Chain: Lt
Molecule details ›
Chain: Lt
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 assembly protein 4 Chain: Ch
Molecule details ›
Chain: Ch
Length: 517 amino acids
Theoretical weight: 57.62 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495
UniProt:
  • Canonical: G0SC29 (Residues: 1-517; Coverage: 100%)
Gene name: CTHT_0055700
Sequence domains: WD domain, G-beta repeat
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:
Large ribosomal subunit protein eL28 Chain: Lq
Molecule details ›
Chain: Lq
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
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 L29 Chain: Lb
Molecule details ›
Chain: Lb
Length: 65 amino acids
Theoretical weight: 7.53 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: Q2H9W4 (Residues: 1-65; Coverage: 100%)
Gene name: CHGG_02990
Sequence domains: Ribosomal L29e protein family
Small ribosomal subunit protein eS32A Chain: Lr
Molecule details ›
Chain: Lr
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermochaetoides thermophila DSM 1495
UniProt:
  • Canonical: P0CX86 (Residues: 1-25; Coverage: 100%)
Gene names: D1290, RPL41A, RPL47A, YDL184C, YL41A
Sequence domains: Ribosomal protein L41
26S rRNA Chain: C1
Molecule details ›
Chain: C1
Length: 3342 nucleotides
Theoretical weight: 1080.78 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: C2
Molecule details ›
Chain: C2
Length: 156 nucleotides
Theoretical weight: 50.15 KDa
Sequence domains: 5.8S ribosomal RNA
5S ribosomal RNA Chain: C4
Molecule details ›
Chain: C4
Length: 119 nucleotides
Theoretical weight: 38.31 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand GTP 2 x GTP
Ligand MG 3 x MG
Ligand ZN 5 x ZN
4 modified residues:
Ligand OMG 10 x OMG
Ligand A2M 8 x A2M
Ligand OMC 8 x OMC
Ligand OMU 8 x OMU

Experiments and Validation Details

Entry percentile scores
Resolution: 2.91Å
Relevant EMDB volumes: EMD-17957
Expression system: Chaetomium thermophilum var. thermophilum DSM 1495

Quick links

Citations

1 citations in other articles

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