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- PDB-5t62: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase L... -

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Basic information

Entry
Database: PDB / ID: 5t62
TitleNmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
Components
  • (60S ribosomal protein ...) x 39
  • 25S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • 60S ribosomal export protein NMD3
  • Eukaryotic translation initiation factor 6
  • Large subunit GTPase 1
  • Ribosomal Protein uL1
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Ribosome Biogenesis / 60S / Nmd3 / Lsg1 / Tif6 / cryo-em
Function / homology
Function and homology information


mating projection tip / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / response to cycloheximide / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits ...mating projection tip / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / response to cycloheximide / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / ribosomal large subunit binding / 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 / protein-RNA complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / protein tag activity / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / protein transport / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ras GTPase GNL1-like / Nmd3, N-terminal / Ribosomal export protein Nmd3 / : / : / NMD3 family / NMD3 OB-fold domain / NMD3 SH3 domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. ...Ras GTPase GNL1-like / Nmd3, N-terminal / Ribosomal export protein Nmd3 / : / : / NMD3 family / NMD3 OB-fold domain / NMD3 SH3 domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / 50S ribosome-binding GTPase / GTP binding domain / Ribosomal protein L29e / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal L29e protein family / : / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L30/YlxQ / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L34e / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal protein L14e domain / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L7A/L8 / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein L32e, conserved site / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L14 / Ribosomal protein L30, N-terminal / Ribosomal protein L6, conserved site-2 / Ribosomal protein L14, KOW motif / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L14 / Ribosomal L37ae protein family / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L6e signature. / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Large ribosomal subunit protein uL15 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL24A / 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 / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Large ribosomal subunit protein eL18A / 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 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / 60S ribosomal export protein NMD3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large subunit GTPase 1 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMalyutin, A.G. / Musalgaonkar, S. / Patchett, S. / Frank, J. / Johnson, A.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53655 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM29169 United States
Howard Hughes Medical Institute (HHMI)HHMI United States
CitationJournal: EMBO J / Year: 2017
Title: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
Authors: Andrey G Malyutin / Sharmishtha Musalgaonkar / Stephanie Patchett / Joachim Frank / Arlen W Johnson /
Abstract: During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. ...During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Apr 12, 2017Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.5Nov 8, 2017Group: Derived calculations / Category: pdbx_struct_assembly
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.6Jun 13, 2018Group: Data collection / Other / Structure summary / Category: cell / entity / struct
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _cell.length_c / _entity.pdbx_description / _struct.pdbx_descriptor
Revision 1.7Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.8Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.9Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
X: Eukaryotic translation initiation factor 6
A: 25S Ribosomal RNA
B: 5S Ribosomal RNA
C: 5.8S Ribosomal RNA
D: 60S ribosomal protein L2-A
E: 60S ribosomal protein L3
F: 60S ribosomal protein L4-A
G: 60S ribosomal protein L5
H: 60S ribosomal protein L6-A
I: 60S ribosomal protein L7-A
J: 60S ribosomal protein L8-A
K: 60S ribosomal protein L9-A
L: 60S ribosomal protein L10
M: 60S ribosomal protein L11-A
N: 60S ribosomal protein L13-A
O: 60S ribosomal protein L14-A
a: 60S ribosomal protein L15-A
b: 60S ribosomal protein L16-A
c: 60S ribosomal protein L17-A
d: 60S ribosomal protein L18-A
e: 60S ribosomal protein L19-A
f: 60S ribosomal protein L20-A
g: 60S ribosomal protein L21-A
h: 60S ribosomal protein L22-A
i: 60S ribosomal protein L23-A
j: 60S ribosomal protein L24-A
k: 60S ribosomal protein L25
l: 60S ribosomal protein L26-A
m: 60S ribosomal protein L27-A
n: 60S ribosomal protein L28
o: 60S ribosomal protein L29
p: 60S ribosomal protein L30
q: 60S ribosomal protein L31-A
r: 60S ribosomal protein L32
s: 60S ribosomal protein L33-A
t: 60S ribosomal protein L34-A
u: 60S ribosomal protein L35-A
v: 60S ribosomal protein L36-A
w: 60S ribosomal protein L37-A
x: 60S ribosomal protein L38
y: 60S ribosomal protein L39
z: Ubiquitin-60S ribosomal protein L40
Q: 60S ribosomal protein L42-A
R: 60S ribosomal protein L43-A
S: Ribosomal Protein uL1
V: 60S ribosomal export protein NMD3
W: Large subunit GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,110,894210
Polymers2,106,40447
Non-polymers4,489163
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area379870 Å2
ΔGint-4424 kcal/mol
Surface area710130 Å2

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Components

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Protein , 5 types, 5 molecules XzSVW

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


Mass: 28597.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TIF6, CDC95, YPR016C, LPZ15C / Plasmid: pAJ3283 / Details (production host): 6HIS-kemptide-TIF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12522
#42: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CH08
#45: Protein Ribosomal Protein uL1 /


Mass: 18485.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#46: Protein 60S ribosomal export protein NMD3 / Nonsense-mediated mRNA decay protein 3


Mass: 59995.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38861
#47: Protein Large subunit GTPase 1


Mass: 71945.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P53145, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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RNA chain , 3 types, 3 molecules ABC

#2: 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: REF: 831416132
#3: RNA chain 5S Ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039024045
#4: 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 (brewer's yeast) / References: GenBank: 1102645687

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60S ribosomal protein ... , 39 types, 39 molecules DEFGHIJKLMNOabcdefghijklmnopqr...

#5: Protein 60S ribosomal protein L2-A / Ribosome / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#6: Protein 60S ribosomal protein L3 / / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#7: Protein 60S ribosomal protein L4-A / Ribosome / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#8: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26321
#9: Protein 60S ribosomal protein L6-A / Ribosome / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02326
#10: Protein 60S ribosomal protein L7-A / Ribosome / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05737
#11: Protein 60S ribosomal protein L8-A / Ribosome / L4 / L4-2 / L7a-1 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P17076
#12: Protein 60S ribosomal protein L9-A / Ribosome / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05738
#13: Protein 60S ribosomal protein L10 / / L9 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


Mass: 25410.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41805
#14: Protein 60S ribosomal protein L11-A / Ribosome / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W9
#15: Protein 60S ribosomal protein L13-A / Ribosome


Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12690
#16: Protein 60S ribosomal protein L14-A / Ribosome


Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36105
#17: Protein 60S ribosomal protein L15-A / Ribosome / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05748
#18: Protein 60S ribosomal protein L16-A / Ribosome / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26784
#19: Protein 60S ribosomal protein L17-A / Ribosome / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05740
#20: Protein 60S ribosomal protein L18-A / Ribosome / RP28


Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX49
#21: Protein 60S ribosomal protein L19-A / Ribosome / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX82
#22: Protein 60S ribosomal protein L20-A / Ribosome / L18a


Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX23
#23: Protein 60S ribosomal protein L21-A / Ribosome


Mass: 18279.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02753
#24: Protein 60S ribosomal protein L22-A / Ribosome / L1c / RP4 / YL31


Mass: 13711.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05749
#25: Protein 60S ribosomal protein L23-A / Ribosome / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX41
#26: Protein 60S ribosomal protein L24-A / Ribosome / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04449
#27: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#28: Protein 60S ribosomal protein L26-A / Ribosome / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05743
#29: Protein 60S ribosomal protein L27-A / Ribosome


Mass: 15568.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#30: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#31: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05747
#32: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#33: Protein 60S ribosomal protein L31-A / Ribosome / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H8
#34: Protein 60S ribosomal protein L32 /


Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38061
#35: Protein 60S ribosomal protein L33-A / Ribosome / L37 / RP47 / YL37


Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05744
#36: Protein 60S ribosomal protein L34-A / Ribosome


Mass: 13673.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P87262
#37: Protein 60S ribosomal protein L35-A / Ribosome


Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX84
#38: Protein 60S ribosomal protein L36-A / Ribosome / L39 / YL39


Mass: 11151.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05745
#39: Protein 60S ribosomal protein L37-A / Ribosome / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49166
#40: Protein 60S ribosomal protein L38 /


Mass: 8845.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#43: Protein 60S ribosomal protein L42-A / Ribosome / L41 / YL27 / YP44


Mass: 12246.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX27
#44: Protein 60S ribosomal protein L43-A / Ribosome / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX25

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Non-polymers , 4 types, 169 molecules

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


Mass: 24.305 Da / Num. of mol.: 160 / Source method: obtained synthetically / Formula: Mg
#49: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#50: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#51: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIn chain 47 the two UNK segments (135-175 and 276-298) are separated by gaps from the rest of the ...In chain 47 the two UNK segments (135-175 and 276-298) are separated by gaps from the rest of the known sequence and there is not enough information in my EM maps to accurately assign neither the number nor sequence to these regions

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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

Component
IDNameTypeEntity IDParent-IDSourceDetails
160S in complex with Nmd3, Lsg1, and Tif6RIBOSOME#1-#470MULTIPLE SOURCES
260S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3COMPLEX#1-#471MULTIPLE SOURCESThis map was acquired by combining 60S-Nmd3 and 60S-Nmd3-Tif6-Lsg1 datasets to increase the number of particles containing 60S-Nmd3 in closed conformation.
Molecular weight
IDEntity assembly-IDUnitsExperimental value
11MEGADALTONSNO
12
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Saccharomyces cerevisiae (brewer's yeast)4932
22Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solution
IDSpecimen-IDpH
117.5
227.5
Specimen
IDExperiment-IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
11NONONOYES
21NONONOYES
Specimen support
IDSpecimen-IDDetailsGrid materialGrid mesh size (divisions/in.)Grid type
1110WGOLD300Made in lab
2210WGOLD300Made in lab
Vitrification
IDInstrumentCryogen nameHumidity (%)Specimen-IDChamber temperature (K)Entry-ID
1FEI VITROBOT MARK IVETHANE10012775T62
2FEI VITROBOT MARK IVETHANE10022775T62

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company /
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELDBright-field microscopy / Specimen-ID: 1

IDAlignment procedureC2 aperture diameter (µm)Calibrated magnification (X)ModelCs (mm)Nominal defocus max (nm)Nominal defocus min (nm)Nominal magnification (X)Specimen holder model
1COMA FREE3031000FEI TECNAI F302.264000150027000OTHER
2FEI TITAN KRIOSFEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Detector modeFilm or detector model
11840COUNTINGGATAN K2 SUMMIT (4k x 4k)
22859.5COUNTINGGATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategoryImage processing-IDImaging-ID
1RELION1.4particle selection1
2Leginonimage acquisition1
4CTFFIND34.0.18CTF correction1
7UCSF Chimeramodel fitting
10Cootmodel refinement
14RELION1.4initial Euler assignment1
15RELION1.4final Euler assignment1
16RELION1.4classification1
17RELION1.43D reconstruction1
27MotionCor208-22-10CTF correction2
30RELION2.0 Open Betainitial Euler assignment2
31RELION2.0 Open Betafinal Euler assignment2
32RELION2.0 Open Betaclassification2
33RELION2.0 Open Beta3D reconstruction2
Image processing
IDImage recording-ID
11
22
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.1FSC 0.143 CUT-OFF22651615T62POINT
23.3FSC 0.143 CUT-OFF1941125T62POINT
Atomic model buildingProtocol: OTHER
RefinementHighest resolution: 3.3 Å
Refinement stepCycle: 1 / Total: 131777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.015143315
ELECTRON MICROSCOPYr_bond_other_d0.0020.0291952
ELECTRON MICROSCOPYr_angle_refined_deg1.0341.539208158
ELECTRON MICROSCOPYr_angle_other_deg1.1913215337
ELECTRON MICROSCOPYr_dihedral_angle_1_deg16.7078.85322998
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.45122.1062365
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.7131510318
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.78115579
ELECTRON MICROSCOPYr_chiral_restr0.1070.21123498
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02106354
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0231969
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.76712.88229293
ELECTRON MICROSCOPYr_mcbond_other5.76712.88129292
ELECTRON MICROSCOPYr_mcangle_it10.57319.29536520
ELECTRON MICROSCOPYr_mcangle_other10.57319.29636521
ELECTRON MICROSCOPYr_scbond_it5.34612.028114022
ELECTRON MICROSCOPYr_scbond_other5.34612.028114023
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other8.97918.08171639
ELECTRON MICROSCOPYr_long_range_B_refined28.252404065
ELECTRON MICROSCOPYr_long_range_B_other28.252404065
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded

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