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- PDB-8fkx: Human nucleolar pre-60S ribosomal subunit (State E) -

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Basic information

Entry
Database: PDB / ID: 8fkx
TitleHuman nucleolar pre-60S ribosomal subunit (State E)
Components
  • (60S ribosomal protein ...) x 28
  • (ATP-dependent RNA helicase ...) x 2
  • (Nucleolar complex protein ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 60S ribosome subunit biogenesis protein NIP7 homolog
  • Eukaryotic translation initiation factor 6
  • GTP-binding protein 4
  • Guanine nucleotide-binding protein-like 3
  • ITS2 rRNA
  • MKI67 FHA domain-interacting nucleolar phosphoprotein
  • Nucleolar protein 16Nucleolus
  • Pescadillo homolog
  • Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
  • Probable rRNA-processing protein EBP2
  • Probable ribosome biogenesis protein RLP24
  • Protein LLP homolog
  • Ribosomal L1 domain-containing protein 1
  • Ribosome biogenesis regulatory protein homolog
  • mRNA turnover protein 4 homolog
  • pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
KeywordsRIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex
Function / homology
Function and homology information


RNA 2'-O-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / RNA metabolic process / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity ...RNA 2'-O-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / RNA metabolic process / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / PeBoW complex / RNA methylation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / miRNA-mediated gene silencing by inhibition of translation / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / positive regulation of telomere maintenance / rRNA base methylation / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / blastocyst formation / TORC2 complex binding / protein localization to nucleolus / GAIT complex / G1 to G0 transition / negative regulation of B cell apoptotic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / rRNA modification in the nucleus and cytosol / A band / nuclear-transcribed mRNA catabolic process / regulation of reactive oxygen species metabolic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / regulation of glycolytic process / negative regulation of ubiquitin protein ligase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / mitotic metaphase chromosome alignment / rRNA metabolic process / maturation of 5.8S rRNA / homeostatic process / stem cell population maintenance / positive regulation of dendritic spine development / lung morphogenesis / macrophage chemotaxis / negative regulation of DNA replication / negative regulation of cell-cell adhesion / fat cell differentiation / ribosomal subunit export from nucleus / Protein hydroxylation / 90S preribosome / regulation of cyclin-dependent protein serine/threonine kinase activity / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / rRNA transcription / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / DNA replication initiation / nucleosome binding / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / Major pathway of rRNA processing in the nucleolus and cytosol / MDM2/MDM4 family protein binding / intracellular estrogen receptor signaling pathway / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / hematopoietic progenitor cell differentiation / negative regulation of intrinsic apoptotic signaling pathway / RNA processing / ribonucleoprotein complex binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / maturation of LSU-rRNA / negative regulation of protein ubiquitination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases
Similarity search - Function
P120R repeat / P120R (NUC006) repeat / DBP10, C-terminal / DDX54/DBP10 family / DBP10CT (NUC160) domain / DBP10CT (NUC160) domain / Nucleolar complex protein 2 / Noc2p family / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 ...P120R repeat / P120R (NUC006) repeat / DBP10, C-terminal / DDX54/DBP10 family / DBP10CT (NUC160) domain / DBP10CT (NUC160) domain / Nucleolar complex protein 2 / Noc2p family / Nucleolar complex-associated protein 3, N-terminal / Nucleolar complex-associated protein 3 / Nucleolar complex-associated protein / MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding / FHA Ki67 binding domain of hNIFK / 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. / Learning associated protein 18-like / Learning-associated protein / 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 biogenesis regulatory protein / Ribosome biogenesis regulatory protein (RRS1) / 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 / : / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) 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 / Ribosomal protein L24e / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / BRCT domain, a BRCA1 C-terminus domain / 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. / Ribosomal protein L6, N-terminal / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L6, N-terminal domain / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / 50S ribosome-binding GTPase / DEAD-box subfamily ATP-dependent helicases signature. / Ribosomal protein L23 / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / Ribosomal L28e/Mak16 / DEAD-box RNA helicase Q motif profile. / Ribosomal L28e protein family / GTP binding domain / PUA-like superfamily / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Pescadillo homolog ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Pescadillo homolog / Ribosomal L1 domain-containing protein 1 / Ribosome biogenesis protein NSA2 homolog / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL14 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Ribosome biogenesis protein BOP1 / Ribosome biogenesis regulatory protein homolog / Ribosomal protein uL30-like / pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 / ATP-dependent RNA helicase DDX54 / Ribosome biogenesis protein BRX1 homolog / Nucleolar complex protein 3 homolog / Probable rRNA-processing protein EBP2 / Protein LLP homolog / Guanine nucleotide-binding protein-like 3 / MKI67 FHA domain-interacting nucleolar phosphoprotein / GTP-binding protein 4 / ATP-dependent RNA helicase DDX18 / Probable ribosome biogenesis protein RLP24 / mRNA turnover protein 4 homolog / 60S ribosome subunit biogenesis protein NIP7 homolog / Nucleolar protein 16 / Nucleolar complex protein 2 homolog / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsVanden Broeck, A. / Klinge, S.
Funding supportEuropean Union, United States, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 711-2019European Union
The G. Harold and Leila Y. Mathers FoundationMF-2104-01554 United States
CitationJournal: Science / Year: 2023
Title: Principles of human pre-60 biogenesis.
Authors: Arnaud Vanden Broeck / Sebastian Klinge /
Abstract: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.
History
DepositionDec 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BA: 60S ribosomal protein L12
BB: 60S ribosomal protein L10a
L1: 5.8S rRNA
L2: ITS2 rRNA
L3: 28S rRNA
L6: 60S ribosomal protein L13
L7: 60S ribosomal protein L13a
L8: 60S ribosomal protein L14
L9: 60S ribosomal protein L15
LA: 60S ribosomal protein L17
LB: 60S ribosomal protein L18
LC: 60S ribosomal protein L18a
LE: 60S ribosomal protein L21
LG: 60S ribosomal protein L23
LH: 60S ribosomal protein L23a
LI: 60S ribosomal protein L26
LK: 60S ribosomal protein L27a
LL: 60S ribosomal protein L28
LN: 60S ribosomal protein L3
LP: 60S ribosomal protein L31
LQ: 60S ribosomal protein L32
LS: 60S ribosomal protein L35
LT: 60S ribosomal protein L35a
LU: 60S ribosomal protein L36
LW: 60S ribosomal protein L37
NA: Nucleolar complex protein 2 homolog
NB: Guanine nucleotide-binding protein-like 3
NF: Ribosome biogenesis protein NSA2 homolog
NH: 60S ribosome subunit biogenesis protein NIP7 homolog
NI: ATP-dependent RNA helicase DDX54
NK: Protein LLP homolog
SA: 60S ribosomal protein L4
SC: 60S ribosomal protein L6
SD: 60S ribosomal protein L7
SE: 60S ribosomal protein L7a
SG: 60S ribosomal protein L9
SH: MKI67 FHA domain-interacting nucleolar phosphoprotein
SI: 60S ribosomal protein L7-like 1
SJ: pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
SK: Eukaryotic translation initiation factor 6
SL: Ribosomal L1 domain-containing protein 1
SM: Pescadillo homolog
SN: Probable rRNA-processing protein EBP2
SO: Ribosome biogenesis protein BRX1 homolog
SQ: mRNA turnover protein 4 homolog
SR: GTP-binding protein 4
SS: Ribosome biogenesis protein BOP1
ST: Ribosome biogenesis regulatory protein homolog
SU: Nucleolar complex protein 3 homolog
SV: Probable ribosome biogenesis protein RLP24
SW: ATP-dependent RNA helicase DDX18
SY: Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
SZ: Nucleolar protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,886,152119
Polymers3,883,62953
Non-polymers2,52366
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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60S ribosomal protein ... , 28 types, 28 molecules BABBL6L7L8L9LALBLCLELGLHLILKLLLNLPLQLSLTLULWSASCSDSESGSI

#1: Protein 60S ribosomal protein L12 / / Large ribosomal subunit protein uL11


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P30050
#2: Protein 60S ribosomal protein L10a / / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62906
#6: Protein 60S ribosomal protein L13 / / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P26373
#7: Protein 60S ribosomal protein L13a / / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P40429
#8: Protein 60S ribosomal protein L14 / / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P50914
#9: Protein 60S ribosomal protein L15 / / Large ribosomal subunit protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P61313
#10: Protein 60S ribosomal protein L17 / / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P18621
#11: Protein 60S ribosomal protein L18 / / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q07020
#12: Protein 60S ribosomal protein L18a / / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q02543
#13: Protein 60S ribosomal protein L21 / / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P46778
#14: Protein 60S ribosomal protein L23 / / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62829
#15: Protein 60S ribosomal protein L23a / / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62750
#16: Protein 60S ribosomal protein L26 / / Large ribosomal subunit protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P61254
#17: Protein 60S ribosomal protein L27a / / Large ribosomal subunit protein uL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P46776
#18: Protein 60S ribosomal protein L28 / / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P46779
#19: Protein 60S ribosomal protein L3 / / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P39023
#20: Protein 60S ribosomal protein L31 / / Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62899
#21: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62910
#22: Protein 60S ribosomal protein L35 / / Large ribosomal subunit protein uL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P42766
#23: Protein 60S ribosomal protein L35a / / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P18077
#24: Protein 60S ribosomal protein L36 / / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y3U8
#25: Protein 60S ribosomal protein L37 / / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P61927
#32: Protein 60S ribosomal protein L4 / / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P36578
#33: Protein 60S ribosomal protein L6 / / Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer ...Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q02878
#34: Protein 60S ribosomal protein L7 / / Large ribosomal subunit protein uL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P18124
#35: Protein 60S ribosomal protein L7a / / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P62424
#36: Protein 60S ribosomal protein L9 / / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P32969
#38: Protein 60S ribosomal protein L7-like 1 / Ribosome / Large ribosomal subunit protein uL30-like 1


Mass: 29730.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q6DKI1

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RNA chain , 3 types, 3 molecules L1L2L3

#3: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 555853
#4: RNA chain ITS2 rRNA


Mass: 376425.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748
#5: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748

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Nucleolar complex protein ... , 2 types, 2 molecules NASU

#26: Protein Nucleolar complex protein 2 homolog / Protein NOC2 homolog / NOC2-like protein / Novel INHAT repressor


Mass: 85028.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y3T9
#49: Protein Nucleolar complex protein 3 homolog / NOC3 protein homolog / Factor for adipocyte differentiation 24 / NOC3-like protein / Nucleolar ...NOC3 protein homolog / Factor for adipocyte differentiation 24 / NOC3-like protein / Nucleolar complex-associated protein 3-like protein


Mass: 92709.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8WTT2

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Protein , 15 types, 15 molecules NBNHNKSHSJSKSLSMSNSQSRSTSVSYSZ

#27: Protein Guanine nucleotide-binding protein-like 3 / E2-induced gene 3 protein / Novel nucleolar protein 47 / NNP47 / Nucleolar GTP-binding protein 3 / ...E2-induced gene 3 protein / Novel nucleolar protein 47 / NNP47 / Nucleolar GTP-binding protein 3 / Nucleostemin


Mass: 62098.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BVP2
#29: Protein 60S ribosome subunit biogenesis protein NIP7 homolog / KD93 / Nucleolar pre-rRNA processing protein NIP7


Mass: 20491.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y221
#31: Protein Protein LLP homolog / Protein LAPS18-like


Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BRT6
#37: Protein MKI67 FHA domain-interacting nucleolar phosphoprotein / Nucleolar phosphoprotein Nopp34 / Nucleolar protein interacting with the FHA domain of pKI-67 / hNIFK


Mass: 34285.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BYG3
#39: Protein pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 / Protein ftsJ homolog 3 / Putative rRNA methyltransferase 3


Mass: 96726.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F
References: UniProt: Q8IY81, Transferases; Transferring one-carbon groups; Methyltransferases
#40: Protein Eukaryotic translation initiation factor 6 / eIF-6 / B(2)GCN homolog / B4 integrin interactor / CAB / p27(BBP)


Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P56537
#41: Protein Ribosomal L1 domain-containing protein 1 / CATX-11 / Cellular senescence-inhibited gene protein / Protein PBK1


Mass: 55089.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O76021
#42: Protein Pescadillo homolog


Mass: 68114.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O00541
#43: Protein Probable rRNA-processing protein EBP2 / EBNA1-binding protein 2 / Nucleolar protein p40


Mass: 34925.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q99848
#45: Protein mRNA turnover protein 4 homolog / Ribosome assembly factor MRTO4


Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9UKD2
#46: Protein GTP-binding protein 4 / Chronic renal failure gene protein / GTP-binding protein NGB / Nucleolar GTP-binding protein 1


Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BZE4
#48: Protein Ribosome biogenesis regulatory protein homolog


Mass: 41278.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q15050
#50: Protein Probable ribosome biogenesis protein RLP24 / Ribosomal L24 domain-containing protein 1 / Ribosomal protein L24-like


Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9UHA3
#52: Protein Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase / Nucleolar protein 1 / Nucleolar protein 2 homolog / Proliferating-cell nucleolar antigen p120 / ...Nucleolar protein 1 / Nucleolar protein 2 homolog / Proliferating-cell nucleolar antigen p120 / Proliferation-associated nucleolar protein p120


Mass: 89441.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F
References: UniProt: P46087, Transferases; Transferring one-carbon groups; Methyltransferases
#53: Protein Nucleolar protein 16 / Nucleolus / HBV pre-S2 trans-regulated protein 3


Mass: 21234.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y3C1

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

#28: Protein Ribosome biogenesis protein NSA2 homolog / / Hairy cell leukemia protein 1 / TGF-beta-inducible nuclear protein 1


Mass: 30136.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O95478
#44: Protein Ribosome biogenesis protein BRX1 homolog / / Brix domain-containing protein 2


Mass: 41483.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8TDN6
#47: Protein Ribosome biogenesis protein BOP1 / / Block of proliferation 1 protein


Mass: 83901.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q14137

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ATP-dependent RNA helicase ... , 2 types, 2 molecules NISW

#30: Protein ATP-dependent RNA helicase DDX54 / ATP-dependent RNA helicase DP97 / DEAD box RNA helicase 97 kDa / DEAD box protein 54


Mass: 98769.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8TDD1, RNA helicase
#51: Protein ATP-dependent RNA helicase DDX18 / DEAD box protein 18 / Myc-regulated DEAD box protein / MrDb


Mass: 75526.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NVP1, RNA helicase

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Non-polymers , 5 types, 66 molecules

#54: Chemical...
ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#56: 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
#57: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#58: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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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: Human nucleolar pre-60S ribosomal subunit (State E) / Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K
Details: Four applications with manual blotting before last blotting with the vitrobot.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 172699
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1RELION4particle selection
2SerialEMimage acquisition
4Gctf1.06CTF correction
9RELION4initial Euler assignment
10cryoSPARC3.3.2final Euler assignment
11RELION4classification
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
20PHENIX1.19.1model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15679142
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126301 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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