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- PDB-6fyx: Structure of a partial yeast 48S preinitiation complex with eIF5 ... -

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Entry
Database: PDB / ID: 6fyx
TitleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)
Components
  • (40S ribosomal protein ...) x 17
  • (Eukaryotic translation initiation factor ...) x 9
  • 18S ribosomal RNA
  • 60S ribosomal protein L41-ARibosome
  • KLLA0A07194p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B06182p
  • KLLA0B08173p
  • KLLA0B11231p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0E12277p
  • KLLA0E23673p
  • KLLA0F07843p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F25542p
  • Ubiquitin-40S ribosomal protein S27a
  • eIF3c,eIF3c
  • mRNA (31-MER)
  • tRNAi
KeywordsRIBOSOME / ribosome / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / eIF5 / tRNAi / 48S PIC / small ribosome subunit
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
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsLlacer, J.L. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Mar 12, 2018 / Release: Dec 5, 2018

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Structure visualization

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Assembly

Deposited unit
1: tRNAi
2: 18S ribosomal RNA
3: mRNA (31-MER)
A: 40S ribosomal protein S0
B: 40S ribosomal protein S1
C: KLLA0F09812p
D: KLLA0D08305p
E: 40S ribosomal protein S4
F: KLLA0D10659p
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: KLLA0E23673p
K: KLLA0B08173p
L: KLLA0A10483p
M: 40S ribosomal protein S12
N: KLLA0F18040p
O: 40S ribosomal protein S14
P: KLLA0F07843p
Q: 40S ribosomal protein S16
R: KLLA0B01474p
S: KLLA0B01562p
T: KLLA0A07194p
U: KLLA0F25542p
V: 40S ribosomal protein S21
W: 40S ribosomal protein S22
X: KLLA0B11231p
Y: 40S ribosomal protein S24
Z: KLLA0B06182p
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ubiquitin-40S ribosomal protein S27a
g: KLLA0E12277p
h: 60S ribosomal protein L41-A
i: Eukaryotic translation initiation factor 1A
j: Eukaryotic translation initiation factor 2 subunit alpha
k: Eukaryotic translation initiation factor 2 subunit gamma
l: Eukaryotic translation initiation factor 2 subunit beta
m: Eukaryotic translation initiation factor 5
o: Eukaryotic translation initiation factor 3 subunit A
p: Eukaryotic translation initiation factor 3 subunit B
q: eIF3c,eIF3c
r: Eukaryotic translation initiation factor 3 subunit G
s: Eukaryotic translation initiation factor 3 subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,762,329171
Polyers1,758,48847
Non-polymers3,841124
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain tRNAi


Mass: 24713.969 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#2: RNA chain 18S ribosomal RNA /


Mass: 579454.875 Da / Num. of mol.: 1
Details: rRNA modifications taken from: http://people.biochem.umass.edu/fournierlab/3dmodmap/ysssu2dframes43d.php
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: GenBank: 49642208
#3: RNA chain mRNA (31-MER)


Mass: 15344.964 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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40S ribosomal protein ... , 17 types, 17 molecules ABEGHIMOQVWYabcde

#4: Protein/peptide 40S ribosomal protein S0 /


Mass: 28264.525 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CN12
#5: Protein/peptide 40S ribosomal protein S1 /


Mass: 29013.678 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWD0
#8: Protein/peptide 40S ribosomal protein S4 /


Mass: 29617.514 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWJ2
#10: Protein/peptide 40S ribosomal protein S6 /


Mass: 26970.391 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CM04
#11: Protein/peptide 40S ribosomal protein S7 /


Mass: 21735.297 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CTD6
#12: Protein/peptide 40S ribosomal protein S8 /


Mass: 22642.727 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CMG3
#16: Protein/peptide 40S ribosomal protein S12 /


Mass: 14466.398 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CLU4
#18: Protein/peptide 40S ribosomal protein S14 / / RP59


Mass: 14530.655 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P27069
#20: Protein/peptide 40S ribosomal protein S16 /


Mass: 15874.531 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q875N2
#25: Protein/peptide 40S ribosomal protein S21 /


Mass: 9797.949 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CXT6
#26: Protein/peptide 40S ribosomal protein S22 /


Mass: 14645.041 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CW21
#28: Protein/peptide 40S ribosomal protein S24 /


Mass: 15194.549 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CU44
#30: Protein/peptide 40S ribosomal protein S26 /


Mass: 13539.957 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CS01
#31: Protein/peptide 40S ribosomal protein S27 /


Mass: 8884.362 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNL2
#32: Protein/peptide 40S ribosomal protein S28 / / S33


Mass: 7549.824 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P33285
#33: Protein/peptide 40S ribosomal protein S29 /


Mass: 6662.570 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CPG3
#34: Protein/peptide 40S ribosomal protein S30 /


Mass: 7141.421 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CUH5

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Protein/peptide , 18 types, 18 molecules CDFJKLNPRSTUXZfghq

#6: Protein/peptide KLLA0F09812p


Mass: 27649.979 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CKL3
#7: Protein/peptide KLLA0D08305p


Mass: 26300.535 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CRK7
#9: Protein/peptide KLLA0D10659p


Mass: 25385.975 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CRA3
#13: Protein/peptide KLLA0E23673p


Mass: 21587.049 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CM18
#14: Protein/peptide KLLA0B08173p


Mass: 12584.377 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CVZ5
#15: Protein/peptide KLLA0A10483p


Mass: 17843.930 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CX80
#17: Protein/peptide KLLA0F18040p


Mass: 16989.875 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CJK0
#19: Protein/peptide KLLA0F07843p


Mass: 15986.796 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CKV4
#21: Protein/peptide KLLA0B01474p


Mass: 15722.216 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWU3
#22: Protein/peptide KLLA0B01562p


Mass: 17084.602 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWT9
#23: Protein/peptide KLLA0A07194p


Mass: 15879.010 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CXM0
#24: Protein/peptide KLLA0F25542p


Mass: 13337.604 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CIM1
#27: Protein/peptide KLLA0B11231p


Mass: 16047.897 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: F2Z602
#29: Protein/peptide KLLA0B06182p


Mass: 12002.116 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CW78
#35: Protein/peptide Ubiquitin-40S ribosomal protein S27a


Mass: 17110.977 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P69061
#36: Protein/peptide KLLA0E12277p


Mass: 35830.945 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNI7
#37: Protein/peptide 60S ribosomal protein L41-A / Ribosome / L47 / Large ribosomal subunit protein eL41-A / YL41


Mass: 3354.243 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P0CX86
#45: Protein/peptide eIF3c,eIF3c


Mass: 86539.539 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32497

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Eukaryotic translation initiation factor ... , 9 types, 9 molecules ijklmoprs

#38: Protein/peptide Eukaryotic translation initiation factor 1A / eIF-1A / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 17462.168 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38912
#39: Protein/peptide Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 34763.652 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20459
#40: Protein/peptide Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 57942.699 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: GCD11, TIF213, YER025W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32481
#41: Protein/peptide Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 31631.309 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUI3, TIF212, YPL237W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P09064
#42: Protein/peptide Eukaryotic translation initiation factor 5 / eIF-5


Mass: 45321.977 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF5, YPR041W, YP3085.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38431
#43: Protein/peptide Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / Translation initiation factor eIF3 / p110 subunit homolog


Mass: 110517.641 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38249
#44: Protein/peptide Eukaryotic translation initiation factor 3 subunit B / eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation initiation factor 3 90 kDa subunit / eIF3 p90 / Translation initiation factor eIF3 p90 subunit


Mass: 88241.766 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PRT1, CDC63, YOR361C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P06103
#46: Protein/peptide Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Translation initiation factor eIF3 p33 subunit homolog / eIF3 p33 homolog


Mass: 30520.502 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF35, SCY_1313 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZZ25
#47: Protein/peptide Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 39 kDa subunit / eIF3 p39


Mass: 38803.375 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TIF34, YMR146C, YM9375.16C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40217

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Non-polymers , 4 types, 124 molecules

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


Mass: 24.305 Da / Num. of mol.: 117 / Formula: Mg / Magnesium
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn / Zinc
#50: Chemical ChemComp-MET / METHIONINE


Mass: 149.211 Da / Num. of mol.: 1 / Formula: C5H11NO2S / Methionine
#51: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Formula: C11H18N5O13P3 / Comment: GMP-PCP (energy-carrying molecule analogue) *YM

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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
IDNameTypeEntity IDParent IDSource
1Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)RIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,470MULTIPLE SOURCES
2RibosomeRIBOSOME2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,371NATURAL
3tRNACOMPLEX11NATURAL
5Initiation factorsCOMPLEX38, 421RECOMBINANT
4Initialtion factorsCOMPLEX39,40,41,43,44,45,46,471RECOMBINANT
6mRNACOMPLEX31RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12284590Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
234932Saccharomyces cerevisiae (baker's yeast)
45559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
34559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
564932Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
15469008Escherichia coli BL21(DE3) (bacteria)
244932Saccharomyces cerevisiae (baker's yeast)
3632630synthetic construct (others)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer ID
120 mMMES1
25 mMMagnessium acetate1
380 mMPotassium acetate1
410 mMAmmonium acetate1
52 mMDithiothreitol (DTT)1
60.001 mMZinc acetate1
70.6 mMATP1
80.25 mMGDPCP1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 / Calibrated magnification: 104478 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 100 kelvins / Temperature (min): 90 kelvins
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 40 e/Å2
Details: Images were collected in movie-mode at 32 frames per second
Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 3 / Number of real images: 3600

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Processing

SoftwareName: REFMAC / Version: 5.8.0166 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2EMANparticle selection
3EPUimage acquisition
5GctfCTF correction
8UCSF Chimera1.1model fitting
9Coot0.8model fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15REFMAC5.8model refinement
Image processingDetails: FEI Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 706713
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 74772 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingOverall b value: 66 / Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: FSC
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1162.5520.110.430.31-0.59-0.220.480.9010.280700.280703.05281.401433260100.0011.4730.1900.2740.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 104332
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.016110961
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.1391.671157775
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg17.1928.22318498
ELECTRON MICROSCOPYr_dihedral_angle_2_deg43.85623.1752709
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.17715.00011353
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.64215.000541
ELECTRON MICROSCOPYr_chiral_restr0.1120.20717887
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02167552
ELECTRON MICROSCOPYr_gen_planes_other
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_it2.78020.18732565
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it5.08930.26140570
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it2.43614.35478396
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined12.563195698
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.05 Å / R factor R work: 0.587 / Lowest resolution: 3.129 Å / Number reflection R free: 0 / Number reflection R work: 106143 / Total number of bins used: 20 / Percent reflection obs: 1

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