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- EMDB-4327: Structure of a partial yeast 48S preinitiation complex with eIF5 ... -

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Entry
Database: EMDB / ID: 4327
TitleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (Map C1)
Map dataFor optimal visualization of eIF2 gamma and beta, gauss-filter the map by 1.1 and display it at 0.03 contour level
SampleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)
  • Ribosome
  • tRNATransfer RNA
  • Initiation factorsInitiation factor
  • Initialtion factors
  • mRNAMessenger RNA
  • (nucleic-acidNucleic acid) x 3
  • (40S ribosomal protein ...) x 17
  • KLLA0F09812p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0E23673p
  • KLLA0B08173p
  • KLLA0A10483p
  • KLLA0F18040p
  • KLLA0F07843p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0A07194p
  • KLLA0F25542p
  • KLLA0B11231p
  • KLLA0B06182p
  • Ubiquitin-40S ribosomal protein S27a
  • KLLA0E12277p
  • 60S ribosomal protein L41-ARibosome
  • (Eukaryotic translation initiation factor ...) x 9
  • eIF3c,eIF3c
  • (ligand) x 4
Function / homologyTranslation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 3 subunit I / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Eukaryotic translation initiation factor 3 subunit C / eIF3B, RNA recognition motif ...Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 3 subunit I / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Eukaryotic translation initiation factor 3 subunit C / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / eIF3G, RNA recognition motif / RNA-binding domain superfamily / Translation initiation factor 2, alpha subunit, middle domain superfamily / RNA-binding S4 domain superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S11 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Eukaryotic translation initiation factor 3 subunit G, N-terminal / Ribosomal protein S7 domain / Elongation factor Tu GTP binding domain / Translation initiation factor 1A (eIF-1A), conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S3, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Eukaryotic translation initiation factor 3 subunit G / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5, N-terminal / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S15P / RNA-binding domain, S1 / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin / Ubiquitin conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein S17e signature. / Eukaryotic translation initiation factor 2 alpha subunit / Eukaryotic translation initiation factor 3 subunit G / Initiation factor eIF2 gamma, C terminal / Eukaryotic translation initiation factor eIF2A / RS4NT (NUC023) domain / Ribosomal S13/S15 N-terminal domain / KH domain / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Ribosomal_S17 N-terminal / Ribosomal protein L41 / Ribosomal protein S30 / Ribosomal protein S5, C-terminal domain / Plectin/S10 domain / S25 ribosomal protein / Elongation factor Tu domain 2 / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7 signature. / Domain found in IF2B/IF5 / Ribosomal protein S24e signature. / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein S19e signature. / Ribosomal protein S5 signature. / Ribosomal protein S6e signature. / Ribosomal protein S3 signature.
Function and homology information
SourceKluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) / Saccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Yeast (fungus)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsLlacer JL / Hussain T / Gordiyenko Y / Ramakrishnan V
CitationJournal: Elife / Year: 2018
Title: Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
Authors: José Luis Llácer / Tanweer Hussain / Adesh K Saini / Jagpreet Singh Nanda / Sukhvir Kaur / Yuliya Gordiyenko / Rakesh Kumar / Alan G Hinnebusch / Jon R Lorsch / V Ramakrishnan
Validation ReportPDB-ID: 6fyx

SummaryFull reportAbout validation report
DateDeposition: Mar 12, 2018 / Header (metadata) release: Aug 24, 2016 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6fyx
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4327.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.34 Å/pix.
= 402. Å
300 pix
1.34 Å/pix.
= 402. Å
300 pix
1.34 Å/pix.
= 402. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.2522875 - 0.52949286
Average (Standard dev.)-0.000008797226 (0.023695989)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 402.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z402.000402.000402.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2520.529-0.000

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Supplemental data

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Sample components

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Entire Structure of a partial yeast 48S preinitiation complex with eIF5 ...

EntireName: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)
Number of components: 57

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Component #1: protein, Structure of a partial yeast 48S preinitiation complex w...

ProteinName: Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)
Recombinant expression: No
MassTheoretical: 1.8 MDa

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Component #2: protein, Ribosome

ProteinName: Ribosome / Recombinant expression: No
SourceSpecies: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)

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Component #3: protein, tRNA

ProteinName: tRNATransfer RNA / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, Initiation factors

ProteinName: Initiation factorsInitiation factor / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #5: protein, Initialtion factors

ProteinName: Initialtion factors / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, mRNA

ProteinName: mRNAMessenger RNA / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: synthetic construct (others)

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Component #7: nucleic-acid, tRNAi

Nucleic-acidName: tRNAi / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGCGCCGU(1MG)(2MG) CGCAG(H2U)GGAA GCGC(M2G)CAGGG CUCAU(T6A)ACCC UGAU(7MG)(H2U)(5MC)(5MC)UC GGAUCG(1MA)AAC CG(RIA)GCGGCGC UACCA
MassTheoretical: 24.713969 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA
Details: rRNA modifications taken from: http://people.biochem.umass.edu/fournierlab/3dmodmap/ysssu2dframes43d.php
Structure: OTHER / Synthetic: No
Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUA(PSU) UUGAUAGUUC CUUUACUACA UGGAUAUCUG UGGUAAUUCU AGAGCUAAUA CAUGCUUAAA AUCUCGACCC UUUGGAAGAG AUGUAUUUAU UAGAUAAAAA AUCAAUGUCU UCGGACUCCU UGAUGAUUCA UAAUAACUUU UCGAAUCGCA UGGCCUUGUG CUGGCGAUGG UUCAUUCAAA UUUCUGCCCU AUCAACUUUC GAUGGUAGGA UAGUGGCCUA CCAUGGUUUC AACGGGUAAC GGGGAAUAAG GGUUCGAUUC CGGAGAGGGA GCCUGAGAAA CGGCUACCAC AUCCAAGGAA GGCAGCAGGC GCGCAAAUUA CCCAAUCCUA AUUCAGGGAG GUAG(PSU)GACAA UAAAUAACGA UACAGGGCCC AUUCGGGUCU UGUAAUUGGA AUGAGUACAA UGUAAAUACC UUAACGAGGA ACAACUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA GUAGCGUAUA UUAAAGUUGU UGCAGUUAAA AAGCUCGUAG UUGAACUUUG GGUCUGGUUG UCCGGUCCGA CUUUAUGUCG CGCACGGUUU UUCAACCGGA UCUUUCCUUC UGGCUAACCU GUACUCCUUG UGGGUGCAGG CGAACCAGGA CUUUUACUUU GAAAAAAUUA GAGUG(PSU)UCAA AGCAGGCGAA AGCUCGAAUA UAUUAGCAUG GAAUAAUGGA AUAGGACGUU UGGUUCUAUU UUGUUGGUUU CUAGGACCAU CGUAAUGAUU AAUAGGGACG GUCGGGGGCA UCAGUAUUCA AUUGUCAGAG GUGAAAUUCU UGGAUUUAUU GAAGACUAAC UACUGCGAAA GCAUUUGCCA AGGACGUUUU CAUUAAUCAA GAACGAAAGU UAGGGGAUCG AAGAUGA(PSU)CA GAUAC(5MC)GUCG UAGUCUUAAC CAUAAACUAU GCCGACUAGG GAUCGGGUGG UGUUUUUCUU AUGACCCACU CGGCACCUUA CGAGAAAUCA AAGUCUUUGG GUUCUGGGGG GAGUAUGGUC GCAAGGCUGA AACUUAAAGG AAUUGACGGA AGGGCACCAC CAGGAGUGGA GCCUGCGGCU UAAUUUGAC(C4J) CAACACGGGG AAACUCACCA GGUCCAGACA CAAUAAGGAU UGACAGAUUG AGAGCUCUUU CUUGAUUUUG UGGGUGGUGG UGCAUGGCCG UUCUUAGU(PSU)G GUGGAGUGAU UUGUCUGCUU AAUUGCGAUA ACGAACGAGA CCUUAACCUA CUAAAUAGGG UUGCUGGCAC UUGCCGGUUG ACUCUUCUUA GAGGGACUAU CGGUUUCAAG CCGAUGGAAG UUUGAGGCAA UAACA(2MG)GUCU GUGAUGCCCU UAGACGUUCU GGGCCGCACG CGCGCUACAC UGACGGAGCC AGCGAGUACA ACCUUGGCCG AGAGGUCUGG GUAAUCUUGU GAAACUCCGU CGUGCUGGGG AUAGAGCAUU GUAAUUAUUG CUCUUCAAC(2MG) AG(7MG)AAUUCCU AGUAAGCGCA AGUCAUCAGC UUGCGUUGAU UACGUCCCUG CCCUUUGUAC ACACCG(5MC)CCG UCGCUAGUAC CGAUUGAAUG GCUUAGUGAG GCCUCAGGAU UUGCUUAGAG AAGGGGGCAA CUCCAUCUCA GAGCGAAGAA UCUGGUCAAA CUUGGUCAUU UAGAGGAACU AAAAGUCGUA ACAAGGUUUC CGUAGGUGA(MA6) CCUGCGGAAG GAUCAUUA
MassTheoretical: 579.454875 kDa
SourceSpecies: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)

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Component #9: nucleic-acid, mRNA (31-MER)

Nucleic-acidName: mRNA (31-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGCUCUCUU CUCUCUCUAA CUAUAAAAAU GUCUCUUCUC UCUCUCGAU
MassTheoretical: 15.344964 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #10: protein, 40S ribosomal protein S0

ProteinName: 40S ribosomal protein S0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.264525 kDa
SourceSpecies: Yeast (fungus)

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Component #11: protein, 40S ribosomal protein S1

ProteinName: 40S ribosomal protein S1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.013678 kDa
SourceSpecies: Yeast (fungus)

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Component #12: protein, KLLA0F09812p

ProteinName: KLLA0F09812p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.649979 kDa
SourceSpecies: Yeast (fungus)

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Component #13: protein, KLLA0D08305p

ProteinName: KLLA0D08305p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.300535 kDa
SourceSpecies: Yeast (fungus)

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Component #14: protein, 40S ribosomal protein S4

ProteinName: 40S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.617514 kDa
SourceSpecies: Yeast (fungus)

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Component #15: protein, KLLA0D10659p

ProteinName: KLLA0D10659p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.385975 kDa
SourceSpecies: Yeast (fungus)

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Component #16: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.970391 kDa
SourceSpecies: Yeast (fungus)

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Component #17: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.735297 kDa
SourceSpecies: Yeast (fungus)

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Component #18: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.642727 kDa
SourceSpecies: Yeast (fungus)

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Component #19: protein, KLLA0E23673p

ProteinName: KLLA0E23673p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.587049 kDa
SourceSpecies: Yeast (fungus)

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Component #20: protein, KLLA0B08173p

ProteinName: KLLA0B08173p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.584377 kDa
SourceSpecies: Yeast (fungus)

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Component #21: protein, KLLA0A10483p

ProteinName: KLLA0A10483p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.84393 kDa
SourceSpecies: Yeast (fungus)

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Component #22: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.466398 kDa
SourceSpecies: Yeast (fungus)

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Component #23: protein, KLLA0F18040p

ProteinName: KLLA0F18040p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.989875 kDa
SourceSpecies: Yeast (fungus)

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Component #24: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.530655 kDa
SourceSpecies: Yeast (fungus)

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Component #25: protein, KLLA0F07843p

ProteinName: KLLA0F07843p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.986796 kDa
SourceSpecies: Yeast (fungus)

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Component #26: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.874531 kDa
SourceSpecies: Yeast (fungus)

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Component #27: protein, KLLA0B01474p

ProteinName: KLLA0B01474p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.722216 kDa
SourceSpecies: Yeast (fungus)

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Component #28: protein, KLLA0B01562p

ProteinName: KLLA0B01562p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.084602 kDa
SourceSpecies: Yeast (fungus)

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Component #29: protein, KLLA0A07194p

ProteinName: KLLA0A07194p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87901 kDa
SourceSpecies: Yeast (fungus)

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Component #30: protein, KLLA0F25542p

ProteinName: KLLA0F25542p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.337604 kDa
SourceSpecies: Yeast (fungus)

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Component #31: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.797949 kDa
SourceSpecies: Yeast (fungus)

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Component #32: protein, 40S ribosomal protein S22

ProteinName: 40S ribosomal protein S22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.645041 kDa
SourceSpecies: Yeast (fungus)

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Component #33: protein, KLLA0B11231p

ProteinName: KLLA0B11231p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.047897 kDa
SourceSpecies: Yeast (fungus)

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Component #34: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.194549 kDa
SourceSpecies: Yeast (fungus)

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Component #35: protein, KLLA0B06182p

ProteinName: KLLA0B06182p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.002116 kDa
SourceSpecies: Yeast (fungus)

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Component #36: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.539957 kDa
SourceSpecies: Yeast (fungus)

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Component #37: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.884362 kDa
SourceSpecies: Yeast (fungus)

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Component #38: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.549824 kDa
SourceSpecies: Yeast (fungus)

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Component #39: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.66257 kDa
SourceSpecies: Yeast (fungus)

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Component #40: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.141421 kDa
SourceSpecies: Yeast (fungus)

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Component #41: protein, Ubiquitin-40S ribosomal protein S27a

ProteinName: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.110977 kDa
SourceSpecies: Yeast (fungus)

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Component #42: protein, KLLA0E12277p

ProteinName: KLLA0E12277p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.830945 kDa
SourceSpecies: Yeast (fungus)

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Component #43: protein, 60S ribosomal protein L41-A

ProteinName: 60S ribosomal protein L41-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.354243 kDa
SourceSpecies: Yeast (fungus)

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Component #44: protein, Eukaryotic translation initiation factor 1A

ProteinName: Eukaryotic translation initiation factor 1A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.462168 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #45: protein, Eukaryotic translation initiation factor 2 subunit alpha

ProteinName: Eukaryotic translation initiation factor 2 subunit alpha
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.763652 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #46: protein, Eukaryotic translation initiation factor 2 subunit gamma

ProteinName: Eukaryotic translation initiation factor 2 subunit gamma
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.942699 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #47: protein, Eukaryotic translation initiation factor 2 subunit beta

ProteinName: Eukaryotic translation initiation factor 2 subunit beta
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.631309 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #48: protein, Eukaryotic translation initiation factor 5

ProteinName: Eukaryotic translation initiation factor 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.321977 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #49: protein, Eukaryotic translation initiation factor 3 subunit A

ProteinName: Eukaryotic translation initiation factor 3 subunit A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 110.517641 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #50: protein, Eukaryotic translation initiation factor 3 subunit B

ProteinName: Eukaryotic translation initiation factor 3 subunit B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 88.241766 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #51: protein, eIF3c,eIF3c

ProteinName: eIF3c,eIF3c / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.539539 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #52: protein, Eukaryotic translation initiation factor 3 subunit G

ProteinName: Eukaryotic translation initiation factor 3 subunit G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.520502 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #53: protein, Eukaryotic translation initiation factor 3 subunit I

ProteinName: Eukaryotic translation initiation factor 3 subunit I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.803375 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #54: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 117 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #55: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #56: ligand, METHIONINE

LigandName: METHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.149211 kDa

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Component #57: ligand, PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

LigandName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.521208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 6.5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000.0 X (nominal), 104478.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm
Specimen HolderModel: OTHER / Temperature: K ( 90.0 - 100.0 K)
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3600
Details: Images were collected in movie-mode at 32 frames per second

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 74772 / Details: FEI Falcon III
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: FSC / Refinement space: RECIPROCAL / Overall bvalue: 66
Output model

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