[English] 日本語
Yorodumi
- PDB-8pv8: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pv8
TitleChaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure
Components
  • (60S ribosomal protein ...) x 29
  • (Nucleolar GTP-binding protein ...) x 2
  • (Pre-rRNA-processing protein ...) x 3
  • (Putative 60S ribosomal ...) x 2
  • (Ribosomal protein ...) x 6
  • (Ribosome biogenesis protein ...) x 2
  • 26S rRNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • DUF2423 domain-containing protein
  • Eukaryotic translation initiation factor 6
  • Large ribosomal subunit protein uL10
  • Protein SDA1
  • Putative GTP binding protein
  • Putative ribosomal protein
  • Ribosomal protein
  • Ribosome assembly protein 4
  • 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 / ribosomal subunit export from nucleus / ribosomal large subunit binding / protein glycosylation / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translation initiation factor activity ...: / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / ribosomal subunit export from nucleus / ribosomal large subunit binding / protein glycosylation / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / rRNA processing / protein transport / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / nucleic acid binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / GTP binding / nucleolus / RNA binding / zinc ion binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Pre-rRNA-processing protein Ipi1, N-terminal / Rix1 complex component involved in 60S ribosome maturation / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / SDA1 domain / Uncharacterised domain NUC130/133, N-terminal / Sda1 / : / SDA1, conserved domain ...Pre-rRNA-processing protein Ipi1, N-terminal / Rix1 complex component involved in 60S ribosome maturation / Pre-rRNA-processing protein RIX1, N-terminal / WD repeat-containing protein WDR18/Ipi3/RID3 / rRNA processing/ribosome biogenesis / SDA1 domain / Uncharacterised domain NUC130/133, N-terminal / Sda1 / : / SDA1, conserved domain / SDA1, HEAT repeat / SDA1, C-terminal / Gcn1, N-terminal / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Centrosomal protein CEP104-like, TOG domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Parkin co-regulated protein / Parkin co-regulated protein / Cgr1-like / Cgr1 family / TOG domain / : / STT3/PglB/AglB core domain / TOG / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Nucleolar GTP-binding protein 2, N-terminal domain / Domain of unknown function DUF2423 / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / Protein of unknown function (DUF2423) / 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 / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / 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 / HEAT repeat profile. / HEAT, type 2 / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 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 / Ribosomal protein L30e / Ribosomal protein L28e / 50S ribosome-binding GTPase / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / GTP binding domain / Ribosomal protein L41 / Ribosomal protein L41 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / : / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L1 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L34Ae / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L34e / Ribosomal protein L31e, conserved site / Ribosomal protein L1 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 / 60S ribosomal protein L27 ...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 / 60S ribosomal protein L14-like protein / Pre-rRNA-processing protein IPI3 / Protein SDA1 / Ribosome biogenesis protein RLP24 / 60S ribosomal protein L2-like protein / Ribosomal protein / 60S ribosomal protein L25-like protein / Pre-rRNA-processing protein RIX1 / 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 / 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 / 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 / 60S ribosomal protein l23-like protein / Pre-rRNA-processing protein IPI1 / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein eL39 / 60S ribosomal protein L29
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 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 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C1: 26S rRNA
C2: 5.8S rRNA
CF: Large ribosomal subunit protein uL10
CH: Nucleolar GTP-binding protein 1
CK: Ribosome biogenesis protein NSA2 homolog
CL: Putative GTP binding 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
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
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein l7-like protein
LG: 60S ribosomal protein L8
LH: 60S ribosomal protein l9-like 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
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
CT: Pre-rRNA-processing protein IPI3
CW: Pre-rRNA-processing protein RIX1
CU: Pre-rRNA-processing protein IPI3
CS: Pre-rRNA-processing protein IPI1
CR: Protein SDA1
Lt: Ribosomal protein
Ch: Ribosome assembly protein 4
LJ: Putative ribosomal protein
LD: 60S ribosomal protein l5-like protein
C4: 5S rRNA
Lq: Putative 60S ribosomal protein
CV: Pre-rRNA-processing protein RIX1
LT: 60S ribosomal protein l21-like protein
Lb: 60S ribosomal protein L29
Lr: 60S ribosomal protein L41-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,121,37670
Polymers3,119,93060
Non-polymers1,44610
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 3 types, 3 molecules C1C2C4

#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 / 5.8S ribosomal RNA


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
#54: RNA chain 5S rRNA / 5S ribosomal RNA


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

-
Protein , 11 types, 11 molecules CFCLCNCOCbCzLhCRLtChLJ

#3: 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
#6: 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
#7: 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
#8: 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
#10: 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
#12: 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
#40: 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
#49: Protein Protein SDA1


Mass: 86963.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S215
#50: Protein Ribosomal protein /


Mass: 24055.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S4Z9
#51: 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
#52: 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

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

#4: 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
#11: 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

-
Ribosome biogenesis protein ... , 2 types, 2 molecules CKCQ

#5: 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
#9: 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

+
60S ribosomal protein ... , 29 types, 29 molecules LALBLCLELFLGLHLKLLLMLOLPLSLULVLXLYLZLaLcLeLfLiLkLpLDLTLbLr

#13: Protein 60S ribosomal protein L2-like protein / Ribosome


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
#14: Protein 60S ribosomal protein L3-like protein / Ribosome


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
#15: Protein 60S ribosomal protein L4-like protein / Ribosome


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
#16: 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
#17: Protein 60S ribosomal protein l7-like protein / Ribosome


Mass: 28821.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFL0
#18: 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
#19: Protein 60S ribosomal protein l9-like protein / Ribosome


Mass: 21568.105 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)
#20: Protein 60S ribosomal protein L12-like protein / Ribosome


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
#21: 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
#22: Protein 60S ribosomal protein L14-like protein / Ribosome


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
#24: Protein 60S ribosomal protein L16-like protein / Ribosome


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
#25: Protein 60S ribosomal protein l17-like protein / Ribosome


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
#28: 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
#29: Protein 60S ribosomal protein L22-like protein / Ribosome


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
#30: Protein 60S ribosomal protein l23-like protein / Ribosome


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
#31: Protein 60S ribosomal protein L25-like protein / Ribosome


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
#32: Protein 60S ribosomal protein L26-like protein / Ribosome


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
#33: 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
#34: Protein 60S ribosomal protein L28-like protein / Ribosome


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)
#35: Protein 60S ribosomal protein l30-like protein / Ribosome


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
#37: Protein 60S ribosomal protein L32-like protein / Ribosome


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
#38: Protein 60S ribosomal protein l33-like protein / Ribosome


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
#41: 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
#43: Protein 60S ribosomal protein L38-like protein / Ribosome


Mass: 9537.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#45: Protein 60S ribosomal protein L43-like protein / Ribosome


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
#53: Protein 60S ribosomal protein l5-like protein / Ribosome


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
#56: Protein 60S ribosomal protein l21-like protein / Ribosome


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
#57: Protein 60S ribosomal protein L29 / / Ribosomal protein eL29


Mass: 7529.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: Q2H9W4
#58: Protein/peptide 60S ribosomal protein L41-A / Ribosome / Ribosomal protein eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: P0CX86

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

#23: 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
#26: Protein Ribosomal protein L18-like protein / Ribosome


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
#27: 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
#39: Protein Ribosomal protein l34-like protein / Ribosome


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
#42: 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
#44: 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

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

#36: 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
#55: 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

-
Pre-rRNA-processing protein ... , 3 types, 5 molecules CTCUCWCVCS

#46: Protein Pre-rRNA-processing protein IPI3


Mass: 47627.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S1T5
#47: Protein Pre-rRNA-processing protein RIX1


Mass: 84849.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S5R0
#48: Protein Pre-rRNA-processing protein IPI1


Mass: 37439.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: P0CT45

-
Non-polymers , 4 types, 14 molecules

#59: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


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


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structureCOMPLEX#1-#580MULTIPLE SOURCES
2RibosomeRIBOSOME#1-#50, #52-#581NATURAL
3Ribosome assembly protein 4COMPLEX#511RECOMBINANT
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

-
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 FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 46 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21061
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: 49.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003173589
ELECTRON MICROSCOPYf_angle_d0.6631250928
ELECTRON MICROSCOPYf_chiral_restr0.039730855
ELECTRON MICROSCOPYf_plane_restr0.006319454
ELECTRON MICROSCOPYf_dihedral_angle_d13.782852837

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more