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- PDB-8pvl: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking... -

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Basic information

Entry
Database: PDB / ID: 8pvl
TitleChaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure
Components
  • (60S ribosomal protein ...) x 27
  • (Nucleolar GTP-binding protein ...) x 2
  • (Putative 60S ribosomal ...) x 2
  • (Ribosomal protein ...) x 6
  • (Ribosome biogenesis protein ...) x 3
  • 26S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DUF2423 domain-containing protein
  • Eukaryotic translation initiation factor 6
  • ITS2
  • Large ribosomal subunit protein uL10
  • Pescadillo homolog
  • Putative GTP binding protein
  • Putative RNA-binding protein
  • Putative ribosomal protein
  • Ribosome assembly protein 4
  • Ribosome biogenesis regulatory protein
  • Ribosome production factor 2 homolog
  • Zinc finger domain-containing protein
  • dolichyl-diphosphooligosaccharide--protein glycotransferase
  • rRNA-processing protein
KeywordsRIBOSOME / biogenesis / pre-60S / 5S RNP
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit binding / protein glycosylation / preribosome, large subunit precursor / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit binding / protein glycosylation / preribosome, large subunit precursor / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cytosolic ribosome assembly / rRNA processing / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / nucleic acid binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTP binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Centromere-binding protein ParB, C-terminal / Centromere-binding protein ParB C-terminal / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Centrosomal protein CEP104-like, TOG domain / Ribosome biogenesis protein Rpf2 / : / STT3/PglB/AglB core domain ...Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Centromere-binding protein ParB, C-terminal / Centromere-binding protein ParB C-terminal / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Centrosomal protein CEP104-like, TOG domain / Ribosome biogenesis protein Rpf2 / : / STT3/PglB/AglB core domain / Ribosome biogenesis protein Nop53/GLTSCR2 / Nop53 (60S ribosomal biogenesis) / Cgr1-like / Cgr1 family / Parkin co-regulated protein / Parkin co-regulated protein / Ribosomal biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / TOG domain / TOG / : / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / Domain of unknown function DUF2423 / YBL028C ribosome biogenesis factor, N-terminal domain / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / HEAT-like repeat / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / : / Pescadillo / Pescadillo N-terminus / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / : / HEAT repeat profile. / HEAT, type 2 / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Brix domain / Brix domain / Brix domain profile. / Brix / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / 50S ribosome-binding GTPase / Ribosomal protein L30e / GTP binding domain / BRCA1 C Terminus (BRCT) domain / Ribosomal protein L28e / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / metallochaperone-like domain / TRASH domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature.
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L3-like protein / 60S ribosomal protein L26-like protein / Ribosomal protein L15 ...GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L3-like protein / 60S ribosomal protein L26-like protein / Ribosomal protein L15 / 60S ribosomal protein L27 / Ribosome biogenesis protein NSA2 homolog / 60S ribosomal protein L6 / dolichyl-diphosphooligosaccharide--protein glycotransferase / 60S ribosomal protein l21-like protein / Ribosomal protein L37 / Putative RNA-binding protein / Putative plasmid related protein / Ribosome biogenesis protein NOP53 / Ribosome biogenesis protein RLP24 / 60S ribosomal protein L2-like protein / 60S ribosomal protein L25-like protein / Large ribosomal subunit protein uL10 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L43-like protein / 60S ribosomal protein L32-like protein / Nucleolar GTP-binding protein 1 / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / Ribosomal protein L19 / 60S ribosomal protein L8 / Zinc finger domain-containing protein / 60S ribosomal protein L36 / Nucleolar GTP-binding protein 2 / Ribosome assembly protein 4 / 60S ribosomal protein L20 / Ribosome biogenesis regulatory protein / 60S ribosomal protein l33-like protein / rRNA-processing protein / Putative 60S ribosomal protein / 60S ribosomal protein L22-like protein / 60S ribosomal protein l5-like protein / 60S ribosomal protein l30-like protein / Putative GTP binding protein / Ribosome production factor 2 homolog / 60S ribosomal protein L4-like protein / 60S ribosomal protein l7-like protein / Ribosomal protein l34-like protein / 60S ribosomal protein L12-like protein / 60S ribosomal protein l17-like protein / 60S ribosomal protein L16-like protein / Large ribosomal subunit protein eL28 / DUF2423 domain-containing protein / Putative ribosomal protein / Pescadillo homolog / 60S ribosomal protein l23-like protein / Large ribosomal subunit protein eL39
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsThoms, M. / Cheng, J. / Denk, T. / Berninghausen, O. / Beckmann, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO Rep / Year: 2023
Title: Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Authors: Matthias Thoms / Benjamin Lau / Jingdong Cheng / Lisa Fromm / Timo Denk / Nikola Kellner / Dirk Flemming / Paulina Fischer / Laurent Falquet / Otto Berninghausen / Roland Beckmann / Ed Hurt /
Abstract: The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from ...The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C1: 26S rRNA
C2: 5.8S rRNA
C3: ITS2
C4: 5S rRNA
CF: Large ribosomal subunit protein uL10
CH: Nucleolar GTP-binding protein 1
CI: Putative RNA-binding protein
CJ: Pescadillo homolog
CK: Ribosome biogenesis protein NSA2 homolog
CL: Putative GTP binding protein
CM: 60S ribosomal protein l7-like protein
CN: Eukaryotic translation initiation factor 6
CO: DUF2423 domain-containing protein
CQ: Ribosome biogenesis protein RLP24
Cb: Zinc finger domain-containing protein
Cd: Nucleolar GTP-binding protein 2
Ce: Ribosome biogenesis protein NOP53
Cf: Ribosome production factor 2 homolog
Cg: Ribosome biogenesis regulatory protein
Ch: Ribosome assembly protein 4
Cz: rRNA-processing protein
LA: 60S ribosomal protein L2-like protein
LB: 60S ribosomal protein L3-like protein
LC: 60S ribosomal protein L4-like protein
LD: 60S ribosomal protein l5-like protein
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein l7-like protein
LG: 60S ribosomal protein L8
LH: 60S ribosomal protein l9-like protein
LJ: Putative ribosomal protein
LK: 60S ribosomal protein L12-like protein
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14-like protein
LN: Ribosomal protein L15
LO: 60S ribosomal protein L16-like protein
LP: 60S ribosomal protein l17-like protein
LQ: Ribosomal protein L18-like protein
LR: Ribosomal protein L19
LS: 60S ribosomal protein L20
LT: 60S ribosomal protein l21-like protein
LU: 60S ribosomal protein L22-like protein
LV: 60S ribosomal protein l23-like protein
LX: 60S ribosomal protein L25-like protein
LY: 60S ribosomal protein L26-like protein
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L28-like protein
Lc: 60S ribosomal protein l30-like protein
Ld: Putative 60S ribosomal protein
Le: 60S ribosomal protein L32-like protein
Lf: 60S ribosomal protein l33-like protein
Lg: Ribosomal protein l34-like protein
Lh: dolichyl-diphosphooligosaccharide--protein glycotransferase
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lk: 60S ribosomal protein L38-like protein
Ll: Ribosomal protein eL39
Lp: 60S ribosomal protein L43-like protein
Lq: Putative 60S ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,020,42968
Polymers3,018,98358
Non-polymers1,44610
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules C1C2C3C4

#1: RNA chain 26S rRNA


Mass: 1080783.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#2: RNA chain 5.8S rRNA


Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: GenBank: MT316345.1
#3: RNA chain ITS2


Mass: 52085.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: GenBank: 1373509168
#4: RNA chain 5S rRNA


Mass: 38312.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)

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Protein , 13 types, 13 molecules CFCICJCLCNCOCbCfCgChCzLJLh

#5: Protein Large ribosomal subunit protein uL10 / Ribosome assembly factor mrt4 / mRNA turnover protein 4


Mass: 30526.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S616
#7: Protein Putative RNA-binding protein


Mass: 45884.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S1H0
#8: Protein Pescadillo homolog / Nucleolar protein 7 homolog


Mass: 77167.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHX6
#10: Protein Putative GTP binding protein


Mass: 61479.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SEW3
#12: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26468.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S683
#13: Protein DUF2423 domain-containing protein


Mass: 13262.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHK0
#15: Protein Zinc finger domain-containing protein


Mass: 13710.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SB32
#18: Protein Ribosome production factor 2 homolog / Ribosome biogenesis protein RPF2 homolog


Mass: 39927.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SF80
#19: Protein Ribosome biogenesis regulatory protein


Mass: 22817.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SCH6
#20: Protein Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


Mass: 57620.664 Da / Num. of mol.: 1 / Mutation: E117D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0055700
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SC29
#21: Protein rRNA-processing protein


Mass: 14710.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SCP3
#29: Protein Putative ribosomal protein


Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHQ2
#51: Protein dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 105169.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase

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Nucleolar GTP-binding protein ... , 2 types, 2 molecules CHCd

#6: Protein Nucleolar GTP-binding protein 1


Mass: 75621.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S8F1
#16: Protein Nucleolar GTP-binding protein 2


Mass: 70313.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SBX1

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Ribosome biogenesis protein ... , 3 types, 3 molecules CKCQCe

#9: Protein Ribosome biogenesis protein NSA2 homolog


Mass: 29724.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S081
#14: Protein Ribosome biogenesis protein RLP24


Mass: 26434.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S497
#17: Protein Ribosome biogenesis protein NOP53


Mass: 50981.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S495

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60S ribosomal protein ... , 27 types, 28 molecules CMLFLALBLCLDLELGLHLKLLLMLOLPLSLTLULVLXLYLZLaLcLeLfLiLkLp

#11: Protein 60S ribosomal protein l7-like protein


Mass: 28821.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFL0
#22: Protein 60S ribosomal protein L2-like protein


Mass: 27598.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S4P8
#23: Protein 60S ribosomal protein L3-like protein


Mass: 44456.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RXW1
#24: Protein 60S ribosomal protein L4-like protein


Mass: 39439.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFC3
#25: Protein 60S ribosomal protein l5-like protein


Mass: 35034.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SEG2
#26: Protein 60S ribosomal protein L6


Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0D6
#27: Protein 60S ribosomal protein L8


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SAJ9
#28: Protein 60S ribosomal protein l9-like protein


Mass: 25867.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This protein component has a sample sequence that does not match the UniProt entry 'G0S0E5' and should not be mapped to any UniProt entry.
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#30: Protein 60S ribosomal protein L12-like protein


Mass: 17802.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SGH8
#31: Protein 60S ribosomal protein L13


Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S992
#32: Protein 60S ribosomal protein L14-like protein


Mass: 16111.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S1R0
#34: Protein 60S ribosomal protein L16-like protein


Mass: 22993.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SH61
#35: Protein 60S ribosomal protein l17-like protein


Mass: 21072.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SGY1
#38: Protein 60S ribosomal protein L20


Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SCE2
#39: Protein 60S ribosomal protein l21-like protein


Mass: 18159.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0Z3
#40: Protein 60S ribosomal protein L22-like protein


Mass: 14302.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SDS8
#41: Protein 60S ribosomal protein l23-like protein


Mass: 14674.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SI44
#42: Protein 60S ribosomal protein L25-like protein


Mass: 17175.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S507
#43: Protein 60S ribosomal protein L26-like protein


Mass: 15565.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RYN9
#44: Protein 60S ribosomal protein L27


Mass: 15803.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RZE9
#45: Protein 60S ribosomal protein L28-like protein


Mass: 16848.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This protein component has a sample sequence that does not match the UniProt entry 'G0SGT6' and should not be mapped to any UniProt entry.
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#46: Protein 60S ribosomal protein l30-like protein


Mass: 11602.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SEI0
#48: Protein 60S ribosomal protein L32-like protein


Mass: 15095.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S6V4
#49: Protein 60S ribosomal protein l33-like protein


Mass: 12330.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SCL3
#52: Protein 60S ribosomal protein L36


Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SBN1
#54: Protein 60S ribosomal protein L38-like protein


Mass: 10902.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#56: Protein 60S ribosomal protein L43-like protein


Mass: 10158.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S6B0

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Ribosomal protein ... , 6 types, 6 molecules LNLQLRLgLjLl

#33: Protein Ribosomal protein L15


Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RZ88
#36: Protein Ribosomal protein L18-like protein


Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S9B5
#37: Protein Ribosomal protein L19


Mass: 317092.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S9T3
#50: Protein Ribosomal protein l34-like protein


Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFN0
#53: Protein Ribosomal protein L37


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S101
#55: Protein Ribosomal protein eL39


Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: Q2H9R2

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Putative 60S ribosomal ... , 2 types, 2 molecules LdLq

#47: Protein Putative 60S ribosomal protein


Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SD68
#57: Protein Putative 60S ribosomal protein


Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHJ6

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Non-polymers , 4 types, 13 molecules

#58: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#59: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structureRIBOSOME#1-#570MULTIPLE SOURCES
2RibosomeRIBOSOME#1-#19, #21-#571NATURAL
3Ribosome assembly protein 4COMPLEX#201RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Thermochaetoides thermophila DSM 1495 (fungus)759272
33Thermochaetoides thermophila DSM 1495 (fungus)759272
Source (recombinant)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 45.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276213
Details: Note: This is a composite structure. Values given for consensus refinement.
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 42.45 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076162774
ELECTRON MICROSCOPYf_angle_d0.9075236023
ELECTRON MICROSCOPYf_chiral_restr0.049928833
ELECTRON MICROSCOPYf_plane_restr0.008517567
ELECTRON MICROSCOPYf_dihedral_angle_d14.591851502

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