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- PDB-8etc: Fkbp39 associated nascent 60S ribosome State 4 -

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Basic information

Entry
Database: PDB / ID: 8etc
TitleFkbp39 associated nascent 60S ribosome State 4
Components
  • (60S ribosomal protein ...) x 31
  • (Ribosome biogenesis protein ...) x 2
  • AdoMet-dependent rRNA methyltransferase spb1
  • Eukaryotic translation initiation factor 6
  • GTPase grn1
  • Probable nucleolar GTP-binding protein 1
  • Protein mak16
  • RNA (147-MER)
  • RNA (2151-MER)
  • Ribosome assembly factor mrt4
  • UPF0642 protein C32H8.05
KeywordsRIBOSOME / 60S Ribosome / nucleophosmin / ribosome biogenesis / fkbp
Function / homology
Function and homology information


L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity ...L13a-mediated translational silencing of Ceruloplasmin expression / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / nuclear-transcribed mRNA catabolic process / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / ribosomal large subunit binding / protein-RNA complex assembly / preribosome, large subunit precursor / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / mitotic spindle / rRNA processing / large ribosomal subunit rRNA binding / protein transport / ribosome biogenesis / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / cell cycle / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mak16 protein / Mak16 protein C-terminal region / 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 / Ribosomal RNA large subunit methyltransferase E / Domain of unknown function DUF2423 / Protein of unknown function (DUF2423) ...Mak16 protein / Mak16 protein C-terminal region / 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 / Ribosomal RNA large subunit methyltransferase E / Domain of unknown function DUF2423 / Protein of unknown function (DUF2423) / Guanine nucleotide-binding protein-like 3, N-terminal domain / GNL3L/Grn1 putative GTPase / 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 / 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 / 50S ribosome-binding GTPase / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / GTP binding domain / 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 L27e, conserved site / : / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / 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 L14e domain / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L7A/L8 / Ribosomal protein L27e signature. / Ribosomal protein L32e, conserved site / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L6, conserved site-2 / Ribosomal protein L14, KOW motif / Ribosomal L30 N-terminal domain / Ribosomal protein L14 / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 60S ribosomal protein L4 C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L24e signature. / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L6e signature. / Ribosomal_L31e / Ribosomal protein L15e, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / AdoMet-dependent rRNA methyltransferase spb1 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A / AdoMet-dependent rRNA methyltransferase spb1 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein uL13B / Large ribosomal subunit protein eL13 / GTPase grn1 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL14 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL36B / Probable nucleolar GTP-binding protein 1 / Large ribosomal subunit protein eL37B / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein uL30B / Large ribosomal subunit protein uL15A / Large ribosomal subunit protein uL3A / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL32A / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL23A / Ribosome biogenesis protein rlp24 / UPF0642 protein C32H8.05 / Large ribosomal subunit protein uL4B / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL33B / Large ribosomal subunit protein eL38A / Ribosome assembly factor mrt4 / Protein mak16 / Large ribosomal subunit protein eL30B / Ribosome biogenesis protein nsa2 / Large ribosomal subunit protein eL21A
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhou, X. / Bilokapic, S. / Deshmukh, A.A. / Halic, M.
Funding support United States, Germany, European Union, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141694 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135599 United States
German Research Foundation (DFG)CryoNucleosome Germany
European Research Council (ERC)ERC-smallRNAhet-309584European Union
CitationJournal: Mol Cell / Year: 2022
Title: Chromatin localization of nucleophosmin organizes ribosome biogenesis.
Authors: Ilaria Ugolini / Silvija Bilokapic / Mylene Ferrolino / Josiah Teague / Yinxia Yan / Xuelin Zhou / Ashish Deshmukh / Michael White / Richard W Kriwacki / Mario Halic /
Abstract: Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin ...Ribosome biogenesis takes place in the nucleolus, a nuclear membrane-less organelle. Although well studied, it remains unknown how nascent ribosomal subunits separate from the central chromatin compartment and move to the outer granular component, where maturation occurs. We find that the Schizosaccharomyces pombe nucleophosmin-like protein Fkbp39 localizes to rDNA sites encoding the 60S subunit rRNA, and this localization contributes to its specific association with nascent 60S subunits. Fkbp39 dissociates from chromatin to bind nascent 60S subunits, causing the latter to partition away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. In vivo, Fkbp39 binding directs the translocation of nascent 60S subunits toward the nucleophosmin-rich granular component. This process increases the efficiency of 60S subunit assembly, facilitating the incorporation of 60S RNA domain III. Thus, chromatin localization determines the specificity of nucleophosmin in sorting nascent ribosomal subunits and coordinates their movement into specialized assembly compartments within the nucleolus.
History
DepositionOct 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: RNA (2151-MER)
2: RNA (147-MER)
3: Protein mak16
8: 60S ribosomal protein L39
B: 60S ribosomal protein L3-A
C: 60S ribosomal protein L4-B
E: 60S ribosomal protein L6
F: 60S ribosomal protein L7-B
G: 60S ribosomal protein L8
H: 60S ribosomal protein L9-A
L: 60S ribosomal protein L13
M: 60S ribosomal protein L14
N: 60S ribosomal protein L15-A
O: 60S ribosomal protein L16-B
P: 60S ribosomal protein L17-A
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
U: 60S ribosomal protein L22
V: 60S ribosomal protein L23-A
W: Ribosome assembly factor mrt4
X: 60S ribosomal protein L25-A
Y: 60S ribosomal protein L26
Z: 60S ribosomal protein L27-A
a: 60S ribosomal protein L28-A
b: Probable nucleolar GTP-binding protein 1
c: 60S ribosomal protein L30-2
d: 60S ribosomal protein L31
e: 60S ribosomal protein L32-A
f: 60S ribosomal protein L33-B
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L35
i: 60S ribosomal protein L36-B
j: 60S ribosomal protein L37-B
k: 60S ribosomal protein L38-1
r: Ribosome biogenesis protein nsa2
s: GTPase grn1
u: Ribosome biogenesis protein rlp24
w: AdoMet-dependent rRNA methyltransferase spb1
y: Eukaryotic translation initiation factor 6
z: UPF0642 protein C32H8.05
T: 60S ribosomal protein L21-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,131,95643
Polymers2,131,89142
Non-polymers651
Water0
1


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

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Components

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RNA chain , 2 types, 2 molecules 12

#1: RNA chain RNA (2151-MER)


Mass: 1129521.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 157310483
#2: RNA chain RNA (147-MER)


Mass: 52880.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 288694

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Protein , 7 types, 7 molecules 3Wbswyz

#3: Protein Protein mak16


Mass: 35686.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTE6
#21: Protein Ribosome assembly factor mrt4 / mRNA turnover protein 4


Mass: 26698.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USZ6
#26: Protein Probable nucleolar GTP-binding protein 1


Mass: 72915.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94659
#37: Protein GTPase grn1 / GTPase in ribosomal export from the nucleolus protein 1 / Nuclear GTP-binding protein grn1


Mass: 52510.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74791
#39: Protein AdoMet-dependent rRNA methyltransferase spb1 / 2'-O-ribose RNA methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase


Mass: 91055.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
References: UniProt: O42832, Transferases; Transferring one-carbon groups; Methyltransferases
#40: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26251.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94476
#41: Protein UPF0642 protein C32H8.05


Mass: 13328.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q96WW3

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60S ribosomal protein ... , 31 types, 31 molecules 8BCEFGHLMNOPQRSUVXYZacdefghijkT

#4: Protein 60S ribosomal protein L39 / / YL36


Mass: 6326.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05767
#5: Protein 60S ribosomal protein L3-A / Ribosome


Mass: 43889.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P40372
#6: Protein 60S ribosomal protein L4-B / Ribosome


Mass: 39982.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P784
#7: Protein 60S ribosomal protein L6 /


Mass: 21285.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79071
#8: Protein 60S ribosomal protein L7-B / Ribosome


Mass: 28499.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P25457
#9: Protein 60S ribosomal protein L8 / / L4 / L7A


Mass: 28659.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13672
#10: Protein 60S ribosomal protein L9-A / Ribosome


Mass: 21544.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10232
#11: Protein 60S ribosomal protein L13 /


Mass: 23578.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74175
#12: Protein 60S ribosomal protein L14 /


Mass: 15241.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94238
#13: Protein 60S ribosomal protein L15-A / Ribosome


Mass: 23862.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74895
#14: Protein 60S ribosomal protein L16-B / Ribosome


Mass: 22215.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42991
#15: Protein 60S ribosomal protein L17-A / Ribosome


Mass: 20854.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14339
#16: Protein 60S ribosomal protein L18-A / Ribosome


Mass: 21240.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10192
#17: Protein 60S ribosomal protein L19-A / Ribosome / YL15


Mass: 22783.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05734
#18: Protein 60S ribosomal protein L20-A / Ribosome / YL17


Mass: 20642.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT68
#19: Protein 60S ribosomal protein L22 /


Mass: 13344.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09668
#20: Protein 60S ribosomal protein L23-A / Ribosome


Mass: 14905.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P0CT60
#22: Protein 60S ribosomal protein L25-A / Ribosome


Mass: 15870.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10330
#23: Protein 60S ribosomal protein L26 /


Mass: 14375.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P78946
#24: Protein 60S ribosomal protein L27-A / Ribosome


Mass: 15421.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14388
#25: Protein 60S ribosomal protein L28-A / Ribosome / L27A / L29


Mass: 16691.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P36585
#27: Protein 60S ribosomal protein L30-2 / Ribosome


Mass: 12261.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTP0
#28: Protein 60S ribosomal protein L31 /


Mass: 13290.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URX6
#29: Protein 60S ribosomal protein L32-A / Ribosome


Mass: 14491.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79015
#30: Protein 60S ribosomal protein L33-B / Ribosome / L37B


Mass: 12133.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USG6
#31: Protein 60S ribosomal protein L34-A / Ribosome


Mass: 12898.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42846
#32: Protein 60S ribosomal protein L35 /


Mass: 14333.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74904
#33: Protein 60S ribosomal protein L36-B / Ribosome


Mass: 11287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94658
#34: Protein 60S ribosomal protein L37-B / Ribosome / L37-2 / YL27


Mass: 10112.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P05733
#35: Protein 60S ribosomal protein L38-1 / Ribosome


Mass: 8511.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USR7
#42: Protein 60S ribosomal protein L21-A / Ribosome


Mass: 18418.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UUC1

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Ribosome biogenesis protein ... , 2 types, 2 molecules ru

#36: Protein Ribosome biogenesis protein nsa2 /


Mass: 29765.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UU79
#38: Protein Ribosome biogenesis protein rlp24 /


Mass: 22323.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10353

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Non-polymers , 1 types, 1 molecules

#43: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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

ComponentName: Fkbp39 associated nascent 60S ribosome State 4 / Type: RIBOSOME / Entity ID: #1-#42 / Source: NATURAL
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003102221
ELECTRON MICROSCOPYf_angle_d0.545149232
ELECTRON MICROSCOPYf_dihedral_angle_d15.50534100
ELECTRON MICROSCOPYf_chiral_restr0.03318627
ELECTRON MICROSCOPYf_plane_restr0.00510522

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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

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