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- PDB-8esr: Ytm1 associated nascent 60S ribosome (-fkbp39) State 2 -

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Basic information

Entry
Database: PDB / ID: 8esr
TitleYtm1 associated nascent 60S ribosome (-fkbp39) State 2
Components
  • (60S ribosomal protein ...) x 32
  • (Ribosome biogenesis protein ...) x 5
  • 25S rRNA (cytosine-C(5))-methyltransferase nop2
  • 60S ribosome subunit biogenesis protein nip7
  • ATP-dependent RNA helicase has1
  • AdoMet-dependent rRNA methyltransferase spb1
  • Eukaryotic translation initiation factor 6
  • GTPase grn1
  • Noc2
  • Nucleolar complex-associated protein 3
  • Nucleolar protein 16
  • Pescadillo homolog
  • Probable nucleolar GTP-binding protein 1
  • Probable rRNA-processing protein ebp2
  • Putative ribosome biogenesis protein C8F11.04
  • RNA (150-MER)
  • RNA (2142-MER)
  • RNA (79-MER)
  • Ribosome assembly factor mrt4
  • UPF0642 protein C32H8.05
  • Uncharacterized RNA-binding protein C1827.05c
KeywordsRIBOSOME / 60S Ribosome / nucleophosmin / ribosome biogenesis / fkbp
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / 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 / 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 / Noc1p-Noc2p complex / Noc2p-Noc3p complex ...Major pathway of rRNA processing in the nucleolus and cytosol / 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 / 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 / Noc1p-Noc2p complex / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / RNA methylation / PeBoW complex / rRNA base methylation / 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 / cell division site / ribosomal large subunit binding / preribosome, large subunit precursor / DNA replication initiation / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / ribosome assembly / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / nuclear periphery / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mitotic spindle / rRNA processing / protein transport / ribosome biogenesis / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / translation / GTPase activity / mRNA binding / chromatin binding / chromatin / nucleolus / GTP binding / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleolar complex protein 2 / Noc2p family / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / WD repeat WDR12/Ytm1 / Ribosome biogenesis factor, NIP7 / RNA (C5-cytosine) methyltransferase, NOP2 / UPF0113, pre-PUA domain / UPF0113 Pre-PUA domain ...Nucleolar complex protein 2 / Noc2p family / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / WD repeat WDR12/Ytm1 / 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 / Eukaryotic rRNA processing / Eukaryotic rRNA processing protein EBP2 / 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 / Domain of unknown function DUF4217 / Domain of unknown function (DUF4217) / DUF4217 / Domain of unknown function DUF2423 / YBL028C ribosome biogenesis factor, N-terminal domain / 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 / Pescadillo / Pescadillo N-terminus / 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 / 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. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / 50S ribosome-binding GTPase / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / GTP binding domain / PUA-like superfamily / 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 / breast cancer carboxy-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Probable rRNA-processing protein ebp2 / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein eL27A ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL8 / Probable rRNA-processing protein ebp2 / 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 / Pescadillo homolog / Large ribosomal subunit protein eL13 / Ribosome biogenesis protein erb1 / GTPase grn1 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein uL29 / Uncharacterized RNA-binding protein C1827.05c / Large ribosomal subunit protein eL14 / 25S rRNA (cytosine-C(5))-methyltransferase nop2 / Nucleolar complex-associated protein 3 / 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 uL30A / 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 / ATP-dependent RNA helicase has1 / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL23A / Ribosome biogenesis protein rlp24 / 60S ribosome subunit biogenesis protein nip7 / UPF0642 protein C32H8.05 / Ribosome biogenesis protein brx1 / Large ribosomal subunit protein uL4B / Uncharacterized NOC2 family protein C1142.04 / Large ribosomal subunit protein eL31 / Ribosome biogenesis protein ytm1 / Large ribosomal subunit protein eL33B / Large ribosomal subunit protein eL38A / Ribosome assembly factor mrt4 / Putative ribosome biogenesis protein C8F11.04 / Large ribosomal subunit protein eL30B / Ribosome biogenesis protein nsa2 / Large ribosomal subunit protein eL21A / Nucleolar protein 16
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 14, 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 (2142-MER)
2: RNA (150-MER)
6: RNA (79-MER)
7: Noc2
8: 60S ribosomal protein L39
A: Ribosome biogenesis protein brx1
B: 60S ribosomal protein L3-A
C: 60S ribosomal protein L4-B
D: ATP-dependent RNA helicase has1
E: 60S ribosomal protein L6
F: 60S ribosomal protein L7-B
G: 60S ribosomal protein L8
H: 60S ribosomal protein L9-A
I: Nucleolar complex-associated protein 3
J: Probable rRNA-processing protein ebp2
K: Putative ribosome biogenesis protein C8F11.04
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
l: 60S ribosome subunit biogenesis protein nip7
m: Ribosome biogenesis protein erb1
n: Pescadillo homolog
o: Uncharacterized RNA-binding protein C1827.05c
p: Ribosome biogenesis protein ytm1
q: 25S rRNA (cytosine-C(5))-methyltransferase nop2
r: Ribosome biogenesis protein nsa2
s: GTPase grn1
t: 60S ribosomal protein L7-A
u: Ribosome biogenesis protein rlp24
v: Nucleolar protein 16
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)2,912,45457
Polymers2,912,38856
Non-polymers651
Water00
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 , 3 types, 3 molecules 126

#1: RNA chain RNA (2142-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 (150-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
#3: RNA chain RNA (79-MER)


Mass: 95732.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: GenBank: 157310483

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Protein , 16 types, 16 molecules 7DIJKWblnoqsvwyz

#4: Protein Noc2


Mass: 81237.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P7G0
#9: Protein ATP-dependent RNA helicase has1


Mass: 65357.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09916, RNA helicase
#14: Protein Nucleolar complex-associated protein 3


Mass: 85236.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94288
#15: Protein Probable rRNA-processing protein ebp2


Mass: 37894.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13802
#16: Protein Putative ribosome biogenesis protein C8F11.04 / U3 snoRNP-associated protein C8F11.04


Mass: 41431.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UT32
#27: 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
#32: 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
#42: Protein 60S ribosome subunit biogenesis protein nip7


Mass: 20892.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q1MTQ9
#44: Protein Pescadillo homolog / Nucleolar protein 7 homolog


Mass: 69294.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O60164
#45: Protein Uncharacterized RNA-binding protein C1827.05c


Mass: 31473.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74978
#47: Protein 25S rRNA (cytosine-C(5))-methyltransferase nop2 / Nucleolar protein 2


Mass: 69029.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast)
References: UniProt: O94268, Transferases; Transferring one-carbon groups; Methyltransferases
#49: 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
#52: Protein Nucleolar protein 16


Mass: 23990.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9Y7Z1
#53: 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
#54: 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
#55: 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 ... , 32 types, 32 molecules 8BCEFGHLMNOPQRSUVXYZacdefghijktT

#5: 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
#7: Protein 60S ribosomal protein L3-A


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


Mass: 39982.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9P784
#10: 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
#11: Protein 60S ribosomal protein L7-B


Mass: 28499.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P25457
#12: 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
#13: Protein 60S ribosomal protein L9-A


Mass: 21544.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10232
#17: 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
#18: 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
#19: Protein 60S ribosomal protein L15-A


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


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


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


Mass: 21240.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10192
#23: Protein 60S ribosomal protein L19-A / 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
#24: Protein 60S ribosomal protein L20-A / 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
#25: 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
#26: Protein 60S ribosomal protein L23-A


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


Mass: 15870.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q10330
#29: 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
#30: Protein 60S ribosomal protein L27-A


Mass: 15421.304 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O14388
#31: Protein 60S ribosomal protein L28-A / 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
#33: Protein 60S ribosomal protein L30-2


Mass: 12261.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9UTP0
#34: 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
#35: Protein 60S ribosomal protein L32-A


Mass: 14491.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P79015
#36: Protein 60S ribosomal protein L33-B / 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
#37: Protein 60S ribosomal protein L34-A


Mass: 12898.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O42846
#38: 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
#39: Protein 60S ribosomal protein L36-B


Mass: 11287.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O94658
#40: Protein 60S ribosomal protein L37-B / 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
#41: Protein 60S ribosomal protein L38-1


Mass: 8511.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9USR7
#50: Protein 60S ribosomal protein L7-A


Mass: 29222.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P17937
#56: Protein 60S ribosomal protein L21-A


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 ... , 5 types, 5 molecules Ampru

#6: Protein Ribosome biogenesis protein brx1


Mass: 33950.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9HGL6
#43: Protein Ribosome biogenesis protein erb1 / Eukaryotic ribosome biogenesis protein 1


Mass: 83052.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O74399
#46: Protein Ribosome biogenesis protein ytm1


Mass: 48388.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q9URY0
#48: 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
#51: 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

#57: 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: Ytm1 associated nascent 60S ribosome (-fkbp39) State 2
Type: RIBOSOME / Entity ID: #1-#3, #5, #4, #6-#56 / 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 FIELD / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002123712
ELECTRON MICROSCOPYf_angle_d0.464178937
ELECTRON MICROSCOPYf_dihedral_angle_d14.79938285
ELECTRON MICROSCOPYf_chiral_restr0.03222373
ELECTRON MICROSCOPYf_plane_restr0.00414202

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