[English] 日本語
Yorodumi
- PDB-8i9z: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i9z
TitleCryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4
Components
  • (60S ribosomal protein ...) x 24
  • (Putative 60S ribosomal ...) x 2
  • (Ribosomal protein ...) x 5
  • (Ribosome biogenesis protein ...) x 5
  • (rRNA-processing ...) x 2
  • 60S ribosomal subunit-like protein
  • 60S ribosome subunit biogenesis protein NIP7
  • ATP-dependent RNA helicase
  • AdoMet-dependent rRNA methyltransferase SPB1
  • Brix domain-containing protein
  • DUF2423 domain-containing protein
  • Eukaryotic translation initiation factor 6
  • Nucleolar GTP-binding protein 1
  • Nucleolar complex-associated protein 3
  • Nucleolar protein 16Nucleolus
  • Pescadillo homolog
  • Putative GTP binding protein
  • Putative NOC2 family protein
  • Putative RNA-binding protein
  • RNA (319-MER)
  • RNA (3341-MER)
  • RNA helicaseHelicase
  • RNA methyltransferase nop2-like protein
  • Ribosomal protein
  • Ribosome assembly factor mrt4
  • dolichyl-diphosphooligosaccharide--protein glycotransferase
KeywordsRIBOSOME / Ribosome biogenesis / pre-60S ribosome
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA methyltransferase activity / rRNA methyltransferase activity / RNA methylation / S-adenosylmethionine-dependent methyltransferase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / ribosomal large subunit binding / protein glycosylation ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA methyltransferase activity / rRNA methyltransferase activity / RNA methylation / S-adenosylmethionine-dependent methyltransferase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / ribosomal large subunit binding / protein glycosylation / preribosome, large subunit precursor / mRNA transport / RNA processing / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome assembly / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / rRNA processing / large ribosomal subunit / ribosome biogenesis / cytosolic large ribosomal subunit / RNA helicase activity / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
60S ribosomal subunit assembly/export protein Loc1 / Nucleolar complex protein 2 / Gcn1, N-terminal / Noc2p family / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / Centrosomal protein CEP104-like, TOG domain / WD repeat WDR12/Ytm1 ...60S ribosomal subunit assembly/export protein Loc1 / Nucleolar complex protein 2 / Gcn1, N-terminal / Noc2p family / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / Centrosomal protein CEP104-like, TOG domain / WD repeat WDR12/Ytm1 / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Ribosome biogenesis factor, NIP7 / RNA (C5-cytosine) methyltransferase, NOP2 / UPF0113, pre-PUA domain / UPF0113 Pre-PUA domain / UPF0113, PUA domain / UPF0113 PUA domain / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / Ribosomal RNA methyltransferase, SPB1-like, C-terminal / Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 / AdoMet-dependent rRNA methyltransferase SPB1-like / Spb1 C-terminal domain / Ribosomal RNA methyltransferase Spb1, DUF3381 / Parkin co-regulated protein / Parkin co-regulated protein / Cgr1-like / Cgr1 family / TOG domain / TOG / Eukaryotic rRNA processing / : / Eukaryotic rRNA processing protein EBP2 / STT3/PglB/AglB core domain / Ribosomal RNA large subunit methyltransferase E / : / Ribosome biogenesis protein BRX1 / CCAAT-binding factor / DDX18/Has1, DEAD-box helicase domain / CBF/Mak21 family / Ribosome biogenesis protein Nop16 / Ribosome biogenesis protein Nop16 / Oligosaccharyl transferase, STT3 subunit / Domain of unknown function DUF4217 / Oligosaccharyl transferase STT3, N-terminal / Domain of unknown function (DUF4217) / DUF4217 / : / Domain of unknown function DUF2423 / Protein of unknown function (DUF2423) / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / NLE / NLE (NUC135) domain / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / HEAT-like repeat / 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. / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L30e / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L28e / DEAD-box subfamily ATP-dependent helicases signature. / 50S ribosome-binding GTPase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L3-like protein / Brix domain-containing protein / ATP-dependent RNA helicase / 60S ribosomal protein L26-like protein ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L3-like protein / Brix domain-containing protein / ATP-dependent RNA helicase / 60S ribosomal protein L26-like protein / ATP-dependent RNA helicase / Ribosomal protein L15 / 60S ribosomal protein L27 / Ribosome biogenesis protein NSA2 homolog / 60S ribosomal protein L6 / dolichyl-diphosphooligosaccharide--protein glycotransferase / 60S ribosomal protein l9-like protein / 60S ribosomal protein l21-like protein / Ribosomal protein L37 / Putative RNA-binding protein / 60S ribosomal protein L14-like protein / 60S ribosome subunit biogenesis protein NIP7 / Ribosome biogenesis protein RLP24 / Ribosomal protein / 60S ribosomal protein L25-like protein / Nucleolar complex-associated protein 3 / Large ribosomal subunit protein uL10 / Eukaryotic translation initiation factor 6 / 60S ribosomal protein L32-like protein / Uncharacterized protein / Nucleolar protein 16 / Nucleolar GTP-binding protein 1 / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / Ribosomal protein L19 / 60S ribosomal protein L8 / 60S ribosomal protein L36 / 60S ribosomal protein L20 / Ribosome biogenesis protein ERB1 / 60S ribosomal protein l33-like protein / rRNA-processing protein / Putative NOC2 family protein / Putative 60S ribosomal protein / 60S ribosomal protein L22-like protein / 60S ribosomal protein l30-like protein / Putative GTP binding protein / Ribosome biogenesis protein YTM1 / 60S ribosomal protein L4-like protein / 60S ribosomal protein l7-like protein / Ribosomal protein l34-like protein / 60S ribosomal protein L38-like protein / rRNA processing protein / Uncharacterized protein / 60S ribosomal protein L12-like protein / 60S ribosomal subunit-like protein / 60S ribosomal protein l17-like protein / 60S ribosomal protein L16-like protein / Large ribosomal subunit protein eL28 / DUF2423 domain-containing protein / RNA methyltransferase nop2-like protein / Pescadillo homolog / 60S ribosomal protein l23-like protein / Large ribosomal subunit protein eL39
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLau, B. / Huang, Z. / Beckmann, R. / Hurt, E. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO Rep / Year: 2023
Title: Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
Authors: Benjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng /
Abstract: Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C1: RNA (3341-MER)
C2: RNA (319-MER)
CA: Brix domain-containing protein
CB: Ribosome biogenesis protein C8F11.04
CC: Ribosome biogenesis protein ERB1
CD: Ribosome biogenesis protein YTM1
CE: RNA helicase
CF: Ribosome assembly factor mrt4
CG: 60S ribosome subunit biogenesis protein NIP7
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
CP: RNA methyltransferase nop2-like protein
CQ: Ribosome biogenesis protein RLP24
CR: Nucleolar protein 16
CS: AdoMet-dependent rRNA methyltransferase SPB1
CT: Nucleolar complex-associated protein 3
CU: rRNA-processing protein EBP2
CV: Putative 60S ribosomal protein
CW: ATP-dependent RNA helicase
CX: 60S ribosomal subunit-like protein
CY: Putative NOC2 family protein
Cz: rRNA-processing 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
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
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: 60S ribosomal protein L39
Lq: Ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,468,45065
Polymers3,467,34460
Non-polymers1,1065
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
RNA chain , 2 types, 2 molecules C1C2

#1: RNA chain RNA (3341-MER)


Mass: 1079977.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 25S rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
#2: RNA chain RNA (319-MER)


Mass: 102607.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 5.8S rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719

-
Protein , 19 types, 19 molecules CACECFCGCHCICJCLCNCOCPCRCSCTCWCXCYLhLq

#3: Protein Brix domain-containing protein


Mass: 36482.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXZ3
#7: Protein RNA helicase / Helicase


Mass: 66830.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYU9
#8: Protein Ribosome assembly factor mrt4 / mRNA turnover protein 4


Mass: 30551.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S616
#9: Protein 60S ribosome subunit biogenesis protein NIP7


Mass: 20685.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S435
#10: Protein Nucleolar GTP-binding protein 1


Mass: 75621.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8F1
#11: Protein Putative RNA-binding protein /


Mass: 45884.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1H0
#12: Protein Pescadillo homolog / Nucleolar protein 7 homolog


Mass: 77167.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHX6
#14: Protein Putative GTP binding protein


Mass: 61523.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEW3
#16: Protein Eukaryotic translation initiation factor 6


Mass: 26468.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S683
#17: Protein DUF2423 domain-containing protein


Mass: 13262.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHK0
#18: Protein RNA methyltransferase nop2-like protein


Mass: 83658.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ0
#20: Protein Nucleolar protein 16 / Nucleolus


Mass: 26960.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S832
#21: Protein AdoMet-dependent rRNA methyltransferase SPB1


Mass: 95510.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGD8
#22: Protein Nucleolar complex-associated protein 3


Mass: 77953.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5L0
#25: Protein ATP-dependent RNA helicase


Mass: 75468.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYG4
#26: Protein 60S ribosomal subunit-like protein /


Mass: 22678.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGJ0
#27: Protein Putative NOC2 family protein


Mass: 89766.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD05
#54: Protein dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 105169.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase
#59: Protein Ribosomal protein /


Mass: 24055.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4Z9

-
Ribosome biogenesis protein ... , 5 types, 5 molecules CBCCCDCKCQ

#4: Protein Ribosome biogenesis protein C8F11.04 /


Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S7X0
#5: Protein Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 90838.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCK6
#6: Protein Ribosome biogenesis protein YTM1 /


Mass: 52989.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFB5
#13: Protein Ribosome biogenesis protein NSA2 homolog /


Mass: 29724.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S081
#19: Protein Ribosome biogenesis protein RLP24 /


Mass: 26434.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S497

+
60S ribosomal protein ... , 24 types, 25 molecules CMLFLBLCLELGLHLKLLLMLOLPLSLTLULVLXLYLZLcLeLfLiLkLl

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


Mass: 28821.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFL0
#29: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXW1
#30: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFC3
#31: Protein 60S ribosomal protein L6 /


Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0D6
#32: Protein 60S ribosomal protein L8 /


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAJ9
#33: Protein 60S ribosomal protein l9-like protein / Ribosome


Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0E5
#34: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGH8
#35: Protein 60S ribosomal protein L13 /


Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S992
#36: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1R0
#38: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SH61
#39: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGY1
#42: Protein 60S ribosomal protein L20 /


Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCE2
#43: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0Z3
#44: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SDS8
#45: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SI44
#46: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S507
#47: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYN9
#48: Protein 60S ribosomal protein L27 /


Mass: 15803.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZE9
#49: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEI0
#51: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6V4
#52: 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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCL3
#55: Protein 60S ribosomal protein L36 /


Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBN1
#57: Protein 60S ribosomal protein L38-like protein / Ribosome


Mass: 9521.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SG89
#58: Protein 60S ribosomal protein L39 /


Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: Q2H9R2

-
RRNA-processing ... , 2 types, 2 molecules CUCz

#23: Protein rRNA-processing protein EBP2


Mass: 50255.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGC2
#28: Protein rRNA-processing protein


Mass: 14710.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCP3

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

#24: Protein Putative 60S ribosomal protein /


Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHJ6
#50: Protein Putative 60S ribosomal protein /


Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD68

-
Ribosomal protein ... , 5 types, 5 molecules LNLQLRLgLj

#37: Protein Ribosomal protein L15 /


Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZ88
#40: Protein Ribosomal protein L18-like protein / Ribosome


Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9B5
#41: Protein Ribosomal protein L19 /


Mass: 317092.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9T3
#53: Protein Ribosomal protein l34-like protein / Ribosome


Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFN0
#56: Protein Ribosomal protein L37 /


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S101

-
Non-polymers , 4 types, 5 molecules

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


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#61: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#62: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#63: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1pre-60S ribosomeRIBOSOME#1-#470NATURAL
2ribosomeRIBOSOME#1-#471NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chaetomium thermophilum (fungus)759272
32Chaetomium thermophilum (fungus)759272
Buffer solutionpH: 7.4
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173028 / Symmetry type: POINT

+
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