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- PDB-6rzz: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles -

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Basic information

Entry
Database: PDB / ID: 6rzz
TitleCryo-EM structures of Lsg1-TAP pre-60S ribosomal particles
Components
  • (60S ribosomal protein ...) x 38
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S ribosomal export protein NMD3
  • Cytoplasmic 60S subunit biogenesis factor REI1
  • Eukaryotic translation initiation factor 6
  • Large subunit GTPase 1
  • Probable metalloprotease ARX1
  • Tyrosine-protein phosphatase YVH1
  • uL1
KeywordsRIBOSOME / 60S subunit / eIF6 / Nmd3 / Lsg1
Function / homology
Function and homology information


budding cell bud growth / preribosome binding / ascospore wall assembly / positive regulation of autophagosome assembly / nucleocytoplasmic transport / protein tyrosine/serine/threonine phosphatase activity / Hydrolases / ribosomal large subunit binding / mating projection tip / ribosomal subunit export from nucleus ...budding cell bud growth / preribosome binding / ascospore wall assembly / positive regulation of autophagosome assembly / nucleocytoplasmic transport / protein tyrosine/serine/threonine phosphatase activity / Hydrolases / ribosomal large subunit binding / mating projection tip / ribosomal subunit export from nucleus / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / ribonucleoprotein complex assembly / response to cycloheximide / cAMP-mediated signaling / regulation of translational fidelity / negative regulation of mRNA splicing, via spliceosome / ribosomal large subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / meiotic cell cycle / protein-tyrosine-phosphatase / metallopeptidase activity / protein dephosphorylation / protein tyrosine phosphatase activity / large ribosomal subunit rRNA binding / cytoplasmic translation / rRNA processing / macroautophagy / ribosome biogenesis / cytoplasmic stress granule / ribosomal large subunit assembly / cytosolic large ribosomal subunit / 5S rRNA binding / mitotic cell cycle / negative regulation of translation / ribosome / rRNA binding / nucleic acid binding / structural constituent of ribosome / sequence-specific DNA binding / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
NMD3 family / Creatinase/aminopeptidase-like / 60S ribosomal protein L4, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Protein-tyrosine phosphatase-like / 50S ribosomal protein L30e-like / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L15 / Ribosomal protein L5, C-terminal ...NMD3 family / Creatinase/aminopeptidase-like / 60S ribosomal protein L4, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Protein-tyrosine phosphatase-like / 50S ribosomal protein L30e-like / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal L18e/L15P superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L19/L19e conserved site / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L15e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L3, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / Dual specificity protein phosphatase domain / Ribosomal protein L5, conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L24e, conserved site / Ribosomal protein L13, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L29, conserved site / Ribosomal protein L32 / Ribosomal protein L21e / Ribosomal protein L22p/L17e / Ribosomal L22e protein family / Ribosomal protein L23 / Ribosomal protein L23, N-terminal domain / KOW motif / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L27e protein family / Ribosomal L29 protein / Ribosomal L29e protein family / Ribosomal protein L30p/L7e / Ribosomal L30 N-terminal domain / Ribosomal protein L31e / Ribosomal protein L35Ae / Ribosomal protein L19e / Ribosomal protein L34e / Ribosomal protein L36e / Ribosomal protein L37e / Ribosomal L38e protein family / Ribosomal L39 protein / Ribosomal protein L44 / Ribosomal L37ae protein family / eIF-6 family / 50S ribosome-binding GTPase / Metallopeptidase family M24 / Dual specificity phosphatase, catalytic domain / C2H2 type zinc-finger (2 copies) / Ribosomal protein L24e / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35A superfamily / Ribosomal protein L3 / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / Ribosomal protein L14
60S ribosomal protein L28 / 60S ribosomal protein L11-A / 60S ribosomal protein L2-A / 60S ribosomal protein L23-A / 60S ribosomal protein L42-A / 60S ribosomal protein L43-A / 60S ribosomal protein L20-A / 60S ribosomal protein L31-A / 60S ribosomal protein L27-A / 60S ribosomal protein L22-A ...60S ribosomal protein L28 / 60S ribosomal protein L11-A / 60S ribosomal protein L2-A / 60S ribosomal protein L23-A / 60S ribosomal protein L42-A / 60S ribosomal protein L43-A / 60S ribosomal protein L20-A / 60S ribosomal protein L31-A / 60S ribosomal protein L27-A / 60S ribosomal protein L22-A / 60S ribosomal protein L19-A / 60S ribosomal protein L15-A / 60S ribosomal protein L36-A / 60S ribosomal protein L33-A / 60S ribosomal protein L26-A / 60S ribosomal protein L17-A / 60S ribosomal protein L9-A / 60S ribosomal protein L7-A / 60S ribosomal protein L39 / 60S ribosomal protein L25 / 60S ribosomal protein L24-A / 60S ribosomal protein L18-A / 60S ribosomal protein L35-A / gb:1331532632: / Large subunit GTPase 1 / gb:1329886537: / gb:834774822: / 60S ribosomal protein L13-A / ORF2 / Probable metalloprotease ARX1 / 60S ribosomal protein L21-A / 60S ribosomal protein L6-A / Tyrosine-protein phosphatase YVH1 / 60S ribosomal protein L34-A / 60S ribosomal protein L38 / 60S ribosomal protein L4-A / 60S ribosomal protein L37-A / 60S ribosomal export protein NMD3 / Cytoplasmic 60S subunit biogenesis factor REI1 / 60S ribosomal protein L32 / 60S ribosomal protein L14-A / 60S ribosomal protein L16-B / 60S ribosomal protein L5 / 60S ribosomal protein L8-A / 60S ribosomal protein L3 / 60S ribosomal protein L30 / 60S ribosomal protein L29
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKargas, V. / Warren, A.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Bloodwise12048 United Kingdom
Medical Research Council (United Kingdom)105161083 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.
Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / ...Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / Leszek Wawiórka / Stefan Mv Freund / Jane L Wagstaff / Antonina Andreeva / Alexandre Faille / Edwin Chen / Florian Stengel / Helmut Bergler / Alan John Warren /
Abstract: During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase ...During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: 25S ribosomal RNA
B: 60S ribosomal protein L2-A
C: 60S ribosomal protein L3
D: 60S ribosomal protein L4-A
E: 60S ribosomal protein L11-A
F: 60S ribosomal protein L9-A
G: 60S ribosomal protein L6-A
H: 60S ribosomal protein L8-A
J: 60S ribosomal protein L16-B
K: 60S ribosomal protein L13-A
L: 60S ribosomal protein L23-A
M: 60S ribosomal protein L14-A
N: 60S ribosomal protein L28
O: 60S ribosomal protein L15-A
P: 60S ribosomal protein L5
Q: 60S ribosomal protein L18-A
R: 60S ribosomal protein L19-A
S: 60S ribosomal protein L20-A
T: 60S ribosomal protein L21-A
U: 60S ribosomal protein L17-A
V: 60S ribosomal protein L22-A
W: 60S ribosomal protein L25
X: 60S ribosomal protein L26-A
Y: 60S ribosomal protein L27-A
Z: 60S ribosomal protein L35-A
a: 60S ribosomal protein L29
b: 60S ribosomal protein L7-A
c: 60S ribosomal protein L30
d: 60S ribosomal protein L31-A
e: 60S ribosomal protein L32
f: 60S ribosomal protein L33-A
g: 60S ribosomal protein L34-A
h: 60S ribosomal protein L36-A
i: 60S ribosomal protein L37-A
j: 60S ribosomal protein L38
k: 60S ribosomal protein L39
l: 60S ribosomal protein L42-A
m: 60S ribosomal protein L43-A
n: Eukaryotic translation initiation factor 6
o: Large subunit GTPase 1
p: uL1
r: Probable metalloprotease ARX1
s: Tyrosine-protein phosphatase YVH1
u: Cytoplasmic 60S subunit biogenesis factor REI1
v: 60S ribosomal protein L24-A
w: 60S ribosomal export protein NMD3
x: 5S ribosomal RNA
y: 5.8S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,216,92858
Polymers2,216,27348
Non-polymers65410
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area365910 Å2
ΔGint-2999 kcal/mol
Surface area670310 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules Axy

#1: RNA chain 25S ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 834774822
#47: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1329886537
#48: 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 (baker's yeast) / References: GenBank: 1331532632

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60S ribosomal protein ... , 38 types, 38 molecules BCDEFGHJKLMNOPQRSTUVWXYZabcdef...

#2: Protein 60S ribosomal protein L2-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX45
#3: 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 (baker's yeast) / References: UniProt: P14126
#4: Protein 60S ribosomal protein L4-A / Ribosome / 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 (baker's yeast) / References: UniProt: P10664
#5: Protein 60S ribosomal protein L11-A / Ribosome / L16 / Large ribosomal subunit protein uL5-A / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C0W9
#6: Protein 60S ribosomal protein L9-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05738
#7: Protein 60S ribosomal protein L6-A / Ribosome / 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 (baker's yeast) / References: UniProt: Q02326
#8: Protein 60S ribosomal protein L8-A / Ribosome / 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 (baker's yeast) / References: UniProt: P17076
#9: Protein 60S ribosomal protein L16-B / Ribosome / L21 / Large ribosomal subunit protein uL13-B / RP23 / YL15


Mass: 22296.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P26785
#10: Protein 60S ribosomal protein L13-A / Ribosome / 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 (baker's yeast) / References: UniProt: Q12690
#11: Protein 60S ribosomal protein L23-A / Ribosome / L17a / Large ribosomal subunit protein uL14-A / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX41
#12: Protein 60S ribosomal protein L14-A / Ribosome / 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 (baker's yeast) / References: UniProt: P36105
#13: Protein 60S ribosomal protein L28 / / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P02406
#14: Protein 60S ribosomal protein L15-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05748
#15: Protein 60S ribosomal protein L5 / / L1 / L1a / Large ribosomal subunit protein uL18 / 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 (baker's yeast) / References: UniProt: P26321
#16: Protein 60S ribosomal protein L18-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX49
#17: Protein 60S ribosomal protein L19-A / Ribosome / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX82
#18: Protein 60S ribosomal protein L20-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX23
#19: Protein 60S ribosomal protein L21-A / Ribosome / Large ribosomal subunit protein eL21-A


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02753
#20: Protein 60S ribosomal protein L17-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05740
#21: Protein 60S ribosomal protein L22-A / Ribosome / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05749
#22: Protein 60S ribosomal protein L25 / / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04456
#23: Protein 60S ribosomal protein L26-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05743
#24: Protein 60S ribosomal protein L27-A / Ribosome / Large ribosomal subunit protein eL27-A


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H6
#25: Protein 60S ribosomal protein L35-A / Ribosome / 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 (baker's yeast) / References: UniProt: P0CX84
#26: Protein 60S ribosomal protein L29 / / Large ribosomal subunit protein eL29 / YL43


Mass: 6691.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P05747
#27: Protein 60S ribosomal protein L7-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05737
#28: Protein 60S ribosomal protein L30 / / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P14120
#29: Protein 60S ribosomal protein L31-A / Ribosome / L34 / Large ribosomal subunit protein eL31-A / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0C2H8
#30: 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 (baker's yeast) / References: UniProt: P38061
#31: Protein 60S ribosomal protein L33-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05744
#32: Protein 60S ribosomal protein L34-A / Ribosome / Large ribosomal subunit protein eL34-A


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P87262
#33: Protein 60S ribosomal protein L36-A / Ribosome / 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 (baker's yeast) / References: UniProt: P05745
#34: Protein 60S ribosomal protein L37-A / Ribosome / 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 (baker's yeast) / References: UniProt: P49166
#35: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P49167
#36: Protein 60S ribosomal protein L39 / / L46 / Large ribosomal subunit protein eL39 / YL40


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04650
#37: Protein 60S ribosomal protein L42-A / Ribosome / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX27
#38: Protein 60S ribosomal protein L43-A / Ribosome / L37a / Large ribosomal subunit protein eL43-A / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P0CX25
#45: Protein 60S ribosomal protein L24-A / Ribosome / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04449

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Protein , 7 types, 7 molecules noprsuw

#39: 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 (baker's yeast) / References: UniProt: Q12522
#40: Protein Large subunit GTPase 1


Mass: 72838.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
References: UniProt: P53145, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#41: Protein uL1


Mass: 17889.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#42: 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 (baker's yeast) / References: UniProt: Q03862, Hydrolases
#43: Protein Tyrosine-protein phosphatase YVH1 / PTPase YVH1


Mass: 41242.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: Q02256, protein-tyrosine-phosphatase
#44: Protein Cytoplasmic 60S subunit biogenesis factor REI1 / Required for isotropic bud growth protein 1 / pre-60S factor REI1


Mass: 45934.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38344
#46: 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 (baker's yeast) / References: UniProt: P38861

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Non-polymers , 1 types, 10 molecules

#49: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 10 / 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: Lsg1-TAP 60s ribosomal subunit / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 63 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4Gctf1.06CTF correction
5CTFFIND4.1CTF correction
8MDFFmodel fitting
10PHENIXmodel refinement
11REFMACmodel refinement
15RELION2.13D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216403 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4V88

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