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- PDB-5t6r: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase L... -

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Entry
Database: PDB / ID: 5t6r
TitleNmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex
Components
  • (60S ribosomal protein ...) x 39
  • 25S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • Maltose binding protein, 60S ribosomal export protein Nmd3 fusion
  • Ribosomal Protein uL1
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Ribosome Biogenesis / 60S / Nmd3 / Lsg1 / Tif6 / cryo-em
Function / homologyRibosomal protein L35A superfamily / Ribosomal protein L21e / 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 protein L35A superfamily / Ribosomal protein L21e / 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 proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L29 protein / Ribosomal L39 protein / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L16p/L10e / Ribosomal protein L6e / Ribosomal protein L31e / Ribosomal protein L34e / Ribosomal protein L24e / Ribosomal protein L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L13e / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L22e protein family / Ribosomal L27e protein family / Ribosomal L29e protein family / Ribosomal L37ae protein family / Ribosomal protein L23 / Ubiquitin family / Ribosomal protein L37e / Ribosomal protein L6, alpha-beta domain superfamily / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 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 protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L34Ae superfamily / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L30/YlxQ / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal L38e protein family / Ribosomal protein L14 / Ribosomal protein L15e core domain superfamily / SCF-beta-TrCP mediated degradation of Emi1 / 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 L15e signature. / Ribosomal protein L10e signature. / Ubiquitin domain profile. / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Ribosomal protein L18e signature. / MAPK6/MAPK4 signaling / Formation of Incision Complex in GG-NER / DNA Damage Recognition in GG-NER / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Metalloprotease DUBs / Ub-specific processing proteases / UCH proteinases / Negative regulation of MAPK pathway / SCF(Skp2)-mediated degradation of p27/p21 / Termination of translesion DNA synthesis / Translesion synthesis by POLI / Translesion synthesis by POLK / AUF1 (hnRNP D0) binds and destabilizes mRNA
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 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 modelOther
1.2Feb 22, 2017Structure modelDatabase references
1.3Apr 12, 2017Structure modelDatabase references
1.4Sep 20, 2017Structure modelAuthor supporting evidence / Data collectionem_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
1.6Jul 18, 2018Structure modelData collectionem_software_em_software.name

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Structure visualization

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Assembly

Deposited unit
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: Maltose binding protein, 60S ribosomal export protein Nmd3 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,050,798134
Polyers2,048,59045
Non-polymers2,20889
Water21612
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)357300
ΔGint (kcal/M)-3667
Surface area (Å2)687040

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain 25S Ribosomal RNA /


Mass: 1097493.875 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 834774822
#2: RNA chain 5S Ribosomal RNA /


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


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1060743159

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

#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#42: 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
#43: 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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Protein/peptide , 3 types, 3 molecules zSV

#41: 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
#44: Protein/peptide Ribosomal Protein uL1 /


Mass: 17889.996 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#45: Protein/peptide Maltose binding protein, 60S ribosomal export protein Nmd3 fusion / Nonsense-mediated mRNA decay protein 3


Mass: 103321.562 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: MBP-TEV-NMD3 / Strain: ATCC 204508 / S288c / References: UniProt: A0A0F8NYV9, UniProt: P38861

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Non-polymers , 3 types, 101 molecules

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


Mass: 24.305 Da / Num. of mol.: 86 / Formula: Mg / Magnesium
#47: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Formula: K / Potassium
#48: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Formula: H2O / Water

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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

ComponentName: 60S in complex with Nmd3 / 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
Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 10W / Grid material: GOLD / Grid mesh size: 300 / Grid type: Made in lab
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 27000 / Calibrated magnification: 31000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm / C2 aperture diameter: 30 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 8 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2Leginonimage acquisition
4CTFFIND34.0.18CTF correction
7UCSF Chimeramodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 65650 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1110.461-0.200.690.620.430.49-0.240.875HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.324270.324274.50264.60357055100.0080.5600.9830.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 126651
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.014138184
ELECTRON MICROSCOPYr_bond_other_d0.0020.02087152
ELECTRON MICROSCOPYr_angle_refined_deg0.9101.522201143
ELECTRON MICROSCOPYr_angle_other_deg1.1783.000204425
ELECTRON MICROSCOPYr_dihedral_angle_1_deg19.2908.98422470
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.41921.9552143
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.39815.0009531
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.70115.000542
ELECTRON MICROSCOPYr_chiral_restr0.1000.21122669
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.020100488
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02030815
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_it2.27812.14626575
ELECTRON MICROSCOPYr_mcbond_other2.27812.14626574
ELECTRON MICROSCOPYr_mcangle_it4.29518.19033140
ELECTRON MICROSCOPYr_mcangle_other4.29518.19033141
ELECTRON MICROSCOPYr_scbond_it1.76811.143111609
ELECTRON MICROSCOPYr_scbond_other1.76811.143111610
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.11116.765168004
ELECTRON MICROSCOPYr_long_range_B_refined11.862399598
ELECTRON MICROSCOPYr_long_range_B_other11.862399599
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 4.5 Å / R factor R work: 0.424 / Lowest resolution: 4.617 Å / Number reflection R free: 0 / Number reflection R work: 26585 / Total number of bins used: 20 / Percent reflection obs: 1

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