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

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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 / Ribosome
Function / homologyRibosomal protein L34Ae superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 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 L34Ae superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ubiquitin domain profile. / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / KOW motif / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal L15 / Ribosomal protein L14 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal L29 protein / Ribosomal protein L15e core domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / 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 L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L32e superfamily / 60S ribosomal protein L4, C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 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 L18e/L15P superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L39 protein / Ribosomal protein L18e, conserved site / Ribosomal protein L1e signature. / Ubiquitin domain signature. / Ribosomal protein L5 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L19e signature. / Ribosomal protein L29 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30 signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L30e signature 1. / Ribosomal protein L13 signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L23 signature. / Ribosomal protein L24e signature. / Ribosomal protein L37e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18e signature. / Ribosomal protein L27e signature. / Ribosomal protein L24 signature. / Ribosomal protein L31e signature. / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L21e signature. / Ribosomal protein L44e signature. / Ribosomal protein L36e signature. / Ribosomal protein L39e signature. / Ribosomal protein L14 signature. / Ribosomal protein L44
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsMalyutin, A.G. / Musalgaonkar, S. / Patchett, S. / Frank, J. / Johnson, A.W.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 2016 / Release: Feb 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 8, 2017Structure modelrepositoryInitial release
1.1Feb 15, 2017Structure modelDatabase references
1.2Feb 22, 2017Structure modelDatabase references
1.3Apr 12, 2017Structure modelDatabase references
1.4Sep 20, 2017Structure modelAuthor supporting evidence / Data collectionem_image_scans / em_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.5Nov 8, 2017Structure modelDerived calculationspdbx_struct_assembly_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
1.6Jun 13, 2018Structure modelData collection / Other / Structure summarycell / entity / struct_cell.length_a / _cell.length_b / _cell.length_c / _entity.pdbx_description / _struct.pdbx_descriptor
1.7Jul 18, 2018Structure modelData collectionem_software_em_software.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-8362
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Structure viewerMolecule:
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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
Polyers2,106,40447
Non-polymers4,489163
Water1086
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)379870
ΔGint (kcal/M)-4424
Surface area (Å2)710130

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Components

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Protein/peptide , 5 types, 5 molecules XzSVW

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


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


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


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


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


Mass: 71945.875 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53145, EC: 3.6.1.-

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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: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132
#3: RNA chain 5S Ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039024045
#4: RNA chain 5.8S Ribosomal RNA /


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1102645687

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

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


Mass: 27463.574 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX45
#6: Protein/peptide 60S ribosomal protein L3 / / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


Mass: 43850.793 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14126
#7: Protein/peptide 60S ribosomal protein L4-A / Ribosome / L2 / RP2 / YL2


Mass: 39159.125 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10664
#8: Protein/peptide 60S ribosomal protein L5 / / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


Mass: 33764.828 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26321
#9: Protein/peptide 60S ribosomal protein L6-A / Ribosome / L17 / RP18 / YL16


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 17661.717 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04449
#27: Protein/peptide 60S ribosomal protein L25 / / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04456
#28: Protein/peptide 60S ribosomal protein L26-A / Ribosome / L33 / YL33


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


Mass: 15568.360 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C2H6
#30: Protein/peptide 60S ribosomal protein L28 / / L27a / L29 / RP44 / RP62 / YL24


Mass: 16761.666 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P02406
#31: Protein/peptide 60S ribosomal protein L29 / / YL43


Mass: 6691.884 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05747
#32: Protein/peptide 60S ribosomal protein L30 / / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14120
#33: Protein/peptide 60S ribosomal protein L31-A / Ribosome / L34 / YL28


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


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


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


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


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


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


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


Mass: 8845.561 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49167
#41: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04650
#43: Protein/peptide 60S ribosomal protein L42-A / Ribosome / L41 / YL27 / YP44


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


Mass: 10112.952 Da / Num. of mol.: 1
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 / Formula: Mg / Magnesium
#49: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Formula: K / Potassium
#50: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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


Mass: 18.015 Da / Num. of mol.: 6 / Formula: H2O / Water

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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 / Reconstruction method: single particle reconstruction

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Sample preparation

Component

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 / Source: MULTIPLE SOURCES

IDNameTypeParent IDDetails
160S in complex with Nmd3, Lsg1, and Tif6RIBOSOME0
260S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3COMPLEX1This 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
IDUnitsEntity assembly IDExperimental value
1MEGADALTONS1NO
12
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
114932Saccharomyces cerevisiae (baker's yeast)
224932Saccharomyces cerevisiae (baker's yeast)
Buffer solution
IDSpecimen IDpH
117.5
227.5
Specimen
IDExperiment IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
11NONONOYES
21NONONOYES
Specimen support
IDSpecimen IDDetailsGrid materialGrid mesh sizeGrid type
1110WGOLD300Made in lab
2210WGOLD300Made in lab
Vitrification

Chamber temperature: 277 kelvins / Cryogen name: ETHANE / Entry ID: 5T62 / Humidity: 100 % / Instrument: FEI VITROBOT MARK IV

IDSpecimen ID
11
22

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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 diameterCalibrated magnificationMicroscope modelCsNominal defocus maxNominal defocus minNominal magnificationSpecimen holder model
1COMA FREE3031000FEI TECNAI F302.264000150027000OTHER
2FEI TITAN KRIOSFEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging IDAverage exposure timeElectron doseDetector modeFilm or detector model
118.040COUNTINGGATAN 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
3D reconstruction

Entry ID: 5T62 / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT

IDResolutionNumber of particlesImage processing ID
13.12265161
23.3194112
Atomic model buildingRef protocol: OTHER
Least-squares processHighest resolution: 3.3 Å
Number of atoms included #1Total: 131777
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.015143315
ELECTRON MICROSCOPYr_bond_other_d0.0020.02091952
ELECTRON MICROSCOPYr_angle_refined_deg1.0341.539208158
ELECTRON MICROSCOPYr_angle_other_deg1.1913.000215337
ELECTRON MICROSCOPYr_dihedral_angle_1_deg16.7078.85322998
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.45122.1062365
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.71315.00010318
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.78115.000579
ELECTRON MICROSCOPYr_chiral_restr0.1070.21123498
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.020106354
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02031969
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_other8.97918.080171639
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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