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- PDB-8hfr: NPC-trapped pre-60S particle -

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Basic information

Entry
Database: PDB / ID: 8hfr
TitleNPC-trapped pre-60S particle
Components
  • (60S ribosomal protein ...) x 37
  • (Nucleolar GTP-binding protein ...) x 2
  • (Ribosome biogenesis protein ...) x 3
  • (YEAST 60S ribosomal protein ...) x 2
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S ribosomal export protein NMD3
  • Bud site selection protein 20
  • Eukaryotic translation initiation factor 6
  • Probable metalloprotease ARX1
  • Ribosome assembly factor MRT4
  • Shuttling pre-60S factor ECM1
  • Translation machinery-associated protein 16
  • UPF0642 protein YBL028C
  • mRNA export factor MEX67
  • mRNA transport regulator MTR2
KeywordsRIBOSOME / pre-60S ribosome
Function / homology
Function and homology information


nuclear RNA export factor complex / regulation of ribosomal subunit export from nucleus / nuclear pore central transport channel / Hydrolases / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...nuclear RNA export factor complex / regulation of ribosomal subunit export from nucleus / nuclear pore central transport channel / Hydrolases / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA processing / pre-mRNA 5'-splice site binding / poly(A)+ mRNA export from nucleus / maturation of 5.8S rRNA / porin activity / response to cycloheximide / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / ATPase activator activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / U1 snRNA binding / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation initiation factor activity / Neutrophil degranulation / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / metallopeptidase activity / rRNA processing / protein transport / ribosome biogenesis / ATPase binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / nucleolus / proteolysis / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Nuclear pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Mex67, RNA recognition motif / RNA recognition motif / Ribosome biogenesis protein Alb1 / Alb1 / Translation machinery-associated protein 16 / Tma16 superfamily / Translation machinery-associated protein 16 ...: / Nuclear pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Mex67, RNA recognition motif / RNA recognition motif / Ribosome biogenesis protein Alb1 / Alb1 / Translation machinery-associated protein 16 / Tma16 superfamily / Translation machinery-associated protein 16 / TAP C-terminal (TAP-C) domain / Nmd3, N-terminal / Ribosomal export protein Nmd3 / : / : / TAP C-terminal domain / NMD3 family / NMD3 OB-fold domain / NMD3 SH3 domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / : / : / Domain of unknown function DUF2423 / YBL028C ribosome biogenesis factor, N-terminal domain / Nucleolar GTP-binding protein 2, N-terminal domain / Nucleolar GTP-binding protein 2 / NGP1NT (NUC091) domain / Nuclear transport factor 2 domain / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / : / GTP-binding protein, orthogonal bundle domain superfamily / Ribosomal biogenesis NSA2 family / Ribosome assembly factor Mrt4 / : / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / 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 / Creatinase/aminopeptidase-like / GTP binding domain / UBA-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 / Ribosomal protein L1, conserved site / NTF2-like domain superfamily / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / : / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L44e / Ribosomal protein L44 / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL11A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13A / Ribosome assembly factor MRT4 / mRNA transport regulator MTR2 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / UPF0642 protein YBL028C / 60S ribosomal export protein NMD3 / Shuttling pre-60S factor ECM1 / Ribosome biogenesis protein NSA2 / Ribosome biogenesis protein ALB1 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Nucleolar GTP-binding protein 2 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Nucleolar GTP-binding protein 1 / Probable metalloprotease ARX1 / Ribosome biogenesis protein RLP24 / Bud site selection protein 20 / Translation machinery-associated protein 16 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A / mRNA export factor MEX67
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLi, Z.Q. / Chen, S.J. / Sui, S.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2023
Title: Nuclear export of pre-60S particles through the nuclear pore complex.
Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Huiqin Xu / Xiaoyun Yang / Peiyi Wang / Ning Gao / Sen-Fang Sui /
Abstract: The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal ...The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC.
History
DepositionNov 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
h1: 60S ribosomal protein L35-A
g2: 60S ribosomal protein L34-A
b3: 60S ribosomal protein L29
B4: 60S ribosomal protein L2-A
V5: 60S ribosomal protein L23-A
O6: 60S ribosomal protein L16-A
f7: 60S ribosomal protein L33-A
F8: 60S ribosomal protein L6-A
v9: Nucleolar GTP-binding protein 2
rA: Nucleolar GTP-binding protein 1
tB: Ribosome biogenesis protein RLP24
cC: 60S ribosomal protein L30
CD: 60S ribosomal protein L3
yE: Eukaryotic translation initiation factor 6
UF: 60S ribosomal protein L22-A
dG: 60S ribosomal protein L31-A
eH: 60S ribosomal protein L32
xI: Shuttling pre-60S factor ECM1
qJ: Ribosome biogenesis protein ALB1
DK: mRNA transport regulator MTR2
LL: 60S ribosomal protein L13-A
KM: YEAST 60S ribosomal protein L12-A
AN: mRNA export factor MEX67
DO: 60S ribosomal protein L4-A
RP: 60S ribosomal protein L19-A
MQ: 60S ribosomal protein L14-A
FR: mRNA transport regulator MTR2
mS: 60S ribosomal protein L42-A
pT: Probable metalloprotease ARX1
YU: 60S ribosomal protein L26-A
vV: 60S ribosomal export protein NMD3
CW: mRNA export factor MEX67
EX: mRNA export factor MEX67
nY: 60S ribosomal protein L43-A
SZ: 60S ribosomal protein L20-A
ia: 60S ribosomal protein L36-A
Ib: 60S ribosomal protein L9-A
Xc: 60S ribosomal protein L25
xd: Ribosome biogenesis protein NSA2
1e: 25S ribosomal RNA
2f: 5S ribosomal RNA
Wg: Ribosome assembly factor MRT4
jh: 60S ribosomal protein L37-A
li: 60S ribosomal protein L39
Hj: 60S ribosomal protein L8-A
Qk: 60S ribosomal protein L18-A
Tl: 60S ribosomal protein L21-A
sm: Translation machinery-associated protein 16
3n: 5.8S ribosomal RNA
No: 60S ribosomal protein L15-A
zp: UPF0642 protein YBL028C
Zq: 60S ribosomal protein L27-A
kr: 60S ribosomal protein L38
As: YEAST 60S ribosomal protein L1-A
Bt: mRNA transport regulator MTR2
Gu: 60S ribosomal protein L7-A
Pv: 60S ribosomal protein L17-A
aw: 60S ribosomal protein L28
ox: Bud site selection protein 20
Jy: 60S ribosomal protein L11-A
Ez: 60S ribosomal protein L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,639,604298
Polymers2,633,84461
Non-polymers5,760237
Water00
1


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

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Components

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60S ribosomal protein ... , 37 types, 37 molecules h1g2b3B4V5O6f7F8cCCDUFdGeHLLDORPMQmSYUnYSZiaIbXcjhliHjQkTlNo...

#1: Protein 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL35A, SOS1, YDL191W, D1249 / Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#2: Protein 60S ribosomal protein L34-A


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL34A, YER056C-A, YER056BC / Strain: ATCC 204508 / S288c / References: UniProt: P87262
#3: Protein 60S ribosomal protein L29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL29, YL43, YFR032C-A, YFR032BW / Strain: ATCC 204508 / S288c / References: UniProt: P05747
#4: Protein 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL2A, RPL5B, YFR031C-A, YFR031BC / Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#5: Protein 60S ribosomal protein L23-A / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713 / Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#6: Protein 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL16A, RPL13, RPL21A, YIL133C / Strain: ATCC 204508 / S288c / References: UniProt: P26784
#7: Protein 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL33A, RPL37A, YPL143W, LPI4W, P2625 / Strain: ATCC 204508 / S288c / References: UniProt: P05744
#8: Protein 60S ribosomal protein L6-A / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL6A, RPL17A, YL16A, YML073C / Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#12: Protein 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL30, RPL32, YGL030W / Strain: ATCC 204508 / S288c / References: UniProt: P14120
#13: Protein 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL3, MAK8, TCM1, YOR063W, YOR29-14 / Strain: ATCC 204508 / S288c / References: UniProt: P14126
#15: Protein 60S ribosomal protein L22-A / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL22A, YLR061W, L2168 / Strain: ATCC 204508 / S288c / References: UniProt: P05749
#16: Protein 60S ribosomal protein L31-A / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL31A, RPL34, RPL34A, YDL075W, D2478 / Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#17: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL32, YBL092W, YBL0838 / Strain: ATCC 204508 / S288c / References: UniProt: P38061
#21: Protein 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL13A, YDL082W / Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#24: Protein 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL4A, RPL2, RPL2A, YBR031W, YBR0315 / Strain: ATCC 204508 / S288c / References: UniProt: P10664
#25: Protein 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC / Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#26: Protein 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL14A, YKL006W, YKL153 / Strain: ATCC 204508 / S288c / References: UniProt: P36105
#27: Protein 60S ribosomal protein L42-A / L41 / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL42A, RPL41A, SCL41A, YNL162W, N1722 / Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#29: Protein 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL26A, RPL26, RPL33A, YLR344W, L8300.4 / Strain: ATCC 204508 / S288c / References: UniProt: P05743
#31: Protein 60S ribosomal protein L43-A / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL43A, YPR043W, YP9499.02 / Strain: ATCC 204508 / S288c / References: UniProt: P0CX25
#32: Protein 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C / Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#33: Protein 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL36A, RPL39A, YMR194W, YM9646.06 / Strain: ATCC 204508 / S288c / References: UniProt: P05745
#34: Protein 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL9A, RPL8A, RPL9, YGL147C / Strain: ATCC 204508 / S288c / References: UniProt: P05738
#35: Protein 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL25, YOL127W / Strain: ATCC 204508 / S288c / References: UniProt: P04456
#40: Protein 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL37A, RPL35A, YLR185W, L9470.6 / Strain: ATCC 204508 / S288c / References: UniProt: P49166
#41: Protein 60S ribosomal protein L39 / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL39, RPL46, SPB2, YJL189W, J0360 / Strain: ATCC 204508 / S288c / References: UniProt: P04650
#42: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL8A, MAK7, RPL4A, YHL033C / Strain: ATCC 204508 / S288c / References: UniProt: P17076
#43: Protein 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL18A, RP28A, YOL120C / Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#44: Protein 60S ribosomal protein L21-A


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL21A, URP1, YBR191W, YBR1401 / Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#47: Protein 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL15A, RPL10A, RPL13A, YL10A, YLR029C / Strain: ATCC 204508 / S288c / References: UniProt: P05748
#49: Protein 60S ribosomal protein L27-A


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL27A, RPL27, YHR010W / Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#50: Protein 60S ribosomal protein L38


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL38, YLR325C, L8543.2 / Strain: ATCC 204508 / S288c / References: UniProt: P49167
#52: Protein 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL7A, RPL6A, RPL8A, YL8A, YGL076C / Strain: ATCC 204508 / S288c / References: UniProt: P05737
#53: Protein 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL17A, RPL17, RPL20A, YKL180W / Strain: ATCC 204508 / S288c / References: UniProt: P05740
#54: Protein 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL28, CYH2, YGL103W / Strain: ATCC 204508 / S288c / References: UniProt: P02406
#56: Protein 60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL11A, RP39A, RPL16A, YPR102C, P8283.14 / Strain: ATCC 204508 / S288c / References: UniProt: P0C0W9
#57: Protein 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL5, RPL1, RPL1A, YPL131W, LPI14W / Strain: ATCC 204508 / S288c / References: UniProt: P26321

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Nucleolar GTP-binding protein ... , 2 types, 2 molecules v9rA

#9: Protein Nucleolar GTP-binding protein 2


Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NOG2, YNR053C, N3484 / Strain: ATCC 204508 / S288c / References: UniProt: P53742
#10: Protein Nucleolar GTP-binding protein 1


Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NOG1, YPL093W, LPG15W / Strain: ATCC 204508 / S288c / References: UniProt: Q02892

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

#11: Protein Ribosome biogenesis protein RLP24 / Ribosomal protein L24-like


Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RLP24, YLR009W / Strain: ATCC 204508 / S288c / References: UniProt: Q07915
#19: Protein Ribosome biogenesis protein ALB1


Mass: 19322.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: ALB1, YJL122W, J0723 / Strain: ATCC 204508 / S288c / References: UniProt: P47019
#36: Protein Ribosome biogenesis protein NSA2 / NOP7-associated protein 2


Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NSA2, YER126C, SYGP-ORF47 / Strain: ATCC 204508 / S288c / References: UniProt: P40078

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Protein , 10 types, 14 molecules yExIDKFRBtANCWEXpTvVWgsmzpox

#14: Protein Eukaryotic translation initiation factor 6 / eIF-6


Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: TIF6, CDC95, YPR016C, LPZ15C / Strain: ATCC 204508 / S288c / References: UniProt: Q12522
#18: Protein Shuttling pre-60S factor ECM1 / Extracellular mutant protein 1 / Protein SIM1


Mass: 23934.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: ECM1, SIM1, YAL059W / Strain: ATCC 204508 / S288c / References: UniProt: P39715
#20: Protein mRNA transport regulator MTR2


Mass: 20802.506 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: MTR2, YKL186C / Strain: ATCC 204508 / S288c / References: UniProt: P34232
#23: Protein mRNA export factor MEX67


Mass: 67417.477 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: MEX67, YPL169C, P2520 / Strain: ATCC 204508 / S288c / References: UniProt: Q99257
#28: Protein Probable metalloprotease ARX1 / Associated with ribosomal export complex protein 1


Mass: 65290.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: ARX1, YDR101C, YD8557.10c / References: UniProt: Q03862, Hydrolases
#30: Protein 60S ribosomal export protein NMD3 / Nonsense-mediated mRNA decay protein 3


Mass: 59167.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: NMD3, YHR170W / Strain: ATCC 204508 / S288c / References: UniProt: P38861
#39: Protein Ribosome assembly factor MRT4 / mRNA turnover protein 4


Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: MRT4, YKL009W, YKL160 / Strain: ATCC 204508 / S288c / References: UniProt: P33201
#45: Protein Translation machinery-associated protein 16


Mass: 20883.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: TMA16, YOR252W / Strain: ATCC 204508 / S288c / References: UniProt: Q08687
#48: Protein UPF0642 protein YBL028C


Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: YBL028C, YBL0423 / Strain: ATCC 204508 / S288c / References: UniProt: P38202
#55: Protein Bud site selection protein 20


Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: BUD20, YLR074C / Strain: ATCC 204508 / S288c / References: UniProt: Q08004

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YEAST 60S ribosomal protein ... , 2 types, 2 molecules KMAs

#22: Protein YEAST 60S ribosomal protein L12-A / L15 / Large ribosomal subunit protein uL11-A / YL23


Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL12A / References: UniProt: P0CX53
#51: Protein YEAST 60S ribosomal protein L1-A / L10a / Large ribosomal subunit protein uL1-A


Mass: 24524.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Genus: RPL1A,SSM1,SSM1A / Strain: ATCC 204508 / S288c / References: UniProt: P0CX43

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RNA chain , 3 types, 3 molecules 1e2f3n

#37: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: NR_132207
#38: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1039023795
#46: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: GenBank: 1669301378

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Non-polymers , 1 types, 237 molecules

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


Mass: 24.305 Da / Num. of mol.: 237 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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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: NPC-trapped pre-60S ribosome / Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86343 / Symmetry type: POINT

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