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

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Entry
Database: PDB / ID: 6fyy
TitleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)
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,Eukaryotic translation initiation factor 3 subunit C
  • mRNA (31-MER)
  • tRNAi
KeywordsRIBOSOME / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / eIF5 / tRNAi / 48S PIC / small ribosome subunit
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / eukaryotic initiation factor eIF2 binding / regulation of fungal-type cell wall biogenesis / conjugation with cellular fusion / translation reinitiation / regulation of eIF2 alpha phosphorylation by amino acid starvation / cytoplasmic translational initiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / eukaryotic initiation factor eIF2 binding / regulation of fungal-type cell wall biogenesis / conjugation with cellular fusion / translation reinitiation / regulation of eIF2 alpha phosphorylation by amino acid starvation / cytoplasmic translational initiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 2B complex / eukaryotic translation initiation factor 3 complex / multi-eIF complex / eukaryotic 43S preinitiation complex / incipient cellular bud site / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / regulation of translational initiation / invasive growth in response to glucose limitation / rRNA export from nucleus / GDP-dissociation inhibitor activity / preribosome, small subunit precursor / mRNA destabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ribosomal small subunit export from nucleus / small-subunit processome / G-protein alpha-subunit binding / ribosomal small subunit binding / mature ribosome assembly / translation initiation factor binding / negative regulation of translational initiation / protein kinase A catalytic subunit binding / translation initiation factor activity / positive regulation of translational fidelity / translational initiation / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / positive regulation of protein autophosphorylation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / protein kinase C binding / small ribosomal subunit / cytoplasmic translation / rRNA processing / protein tag / cytoplasmic stress granule / cytosolic large ribosomal subunit / ribosome binding / double-stranded RNA binding / cytosolic small ribosomal subunit / regulation of G2/M transition of mitotic cell cycle / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / GTPase activity / G protein-coupled receptor signaling pathway / GTP binding / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Eukaryotic translation initiation factor 3 subunit G / Ribosomal protein S10 domain / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA-binding domain, S1 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily ...Eukaryotic translation initiation factor 3 subunit G / Ribosomal protein S10 domain / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / RNA-binding domain, S1 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 3 subunit G, N-terminal / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2, eukaryotic / Ribosomal protein S5 domain 2-type fold / 40S ribosomal protein S4, C-terminal domain / WD40-repeat-containing domain superfamily / Ribosomal protein S8 superfamily / RNA-binding domain superfamily / eIF3B, RNA recognition motif / eIF3G, RNA recognition motif / 40S ribosomal protein S11, N-terminal / Ubiquitin-like domain superfamily / 40S ribosomal protein S1/3, eukaryotes / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit A / Ribosomal protein S9, conserved site / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / Ribosomal protein S4, conserved site / Ribosomal protein S4e, central region / Translation initiation factor, beta propellor-like domain / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Translation initiation factor 2, gamma subunit, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / MIF4G-like domain superfamily / Armadillo-type fold / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Eukaryotic translation initiation factor 3 subunit G / WD40-repeat-containing domain / Ribosomal S24e conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ubiquitin domain / Ubiquitin conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S21e, conserved site / Ribosomal S11, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Translation initiation factor 1A (eIF-1A), conserved site / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S9/S16 / Ribosomal S17 / Ribosomal protein S13/S18 / Ribosomal protein S19e / Ribosomal protein S10p/S20e / Ribosomal protein S21e / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S24e / S25 ribosomal protein / Ribosomal protein S26e / Ribosomal protein S27 / Ribosomal protein S28e / Ribosomal protein S30 / Ribosomal S13/S15 N-terminal domain / Elongation factor Tu domain 2 / PCI domain / Eukaryotic translation initiation factor eIF2A / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / eIF4-gamma/eIF5/eIF2-epsilon / Domain found in IF2B/IF5 / Initiation factor eIF2 gamma, C terminal / Elongation factor Tu GTP binding domain / Ubiquitin family / Eukaryotic translation initiation factor 2 alpha subunit / S1 RNA binding domain / Translation initiation factor 1A / IF-1
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 5 / Eukaryotic translation initiation factor 2 subunit beta / Eukaryotic translation initiation factor 3 subunit A / 60S ribosomal protein L41-A / Eukaryotic translation initiation factor 2 subunit alpha / Eukaryotic translation initiation factor 2 subunit gamma ...Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 5 / Eukaryotic translation initiation factor 2 subunit beta / Eukaryotic translation initiation factor 3 subunit A / 60S ribosomal protein L41-A / Eukaryotic translation initiation factor 2 subunit alpha / Eukaryotic translation initiation factor 2 subunit gamma / 40S ribosomal protein S28 / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 1A / KLLA0E12277p / Ubiquitin-40S ribosomal protein S27a / KLLA0B01474p / 40S ribosomal protein S29 / KLLA0D10659p / KLLA0D08305p / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / 40S ribosomal protein S22 / 40S ribosomal protein S25 / 40S ribosomal protein S1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0A10483p / KLLA0F25542p / KLLA0A07194p / 40S ribosomal protein S21 / 40S ribosomal protein S16 / gb:49642208: / 40S ribosomal protein S0 / 40S ribosomal protein S8 / KLLA0E23673p / 40S ribosomal protein S6 / 40S ribosomal protein S12 / KLLA0F07843p / KLLA0F09812p / KLLA0F18040p / 40S ribosomal protein S27 / 40S ribosomal protein S14
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLlacer, J.L. / Hussain, T. / Gordiyenko, Y. / Ramakrishnan, V.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
FEBS United Kingdom
CitationJournal: Elife / Year: 2018
Title: Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
Authors: Jose Luis Llácer / Tanweer Hussain / Adesh K Saini / Jagpreet Singh Nanda / Sukhvir Kaur / Yuliya Gordiyenko / Rakesh Kumar / Alan G Hinnebusch / Jon R Lorsch / V Ramakrishnan /
Abstract: In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA in a 'P' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) ...In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA in a 'P' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNA. Substitutions of eIF5 residues involved in the eIF5-NTD/tRNA interaction influenced initiation at near-cognate UUG codons and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn
Item: _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jul 31, 2019Group: Data collection / Refinement description / Category: refine
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
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,Eukaryotic translation initiation factor 3 subunit C
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)1,762,414171
Polymers1,758,57347
Non-polymers3,841124
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area276650 Å2
ΔGint-2952 kcal/mol
Surface area528760 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain tRNAi


Mass: 24799.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#2: RNA chain 18S ribosomal RNA /


Mass: 579454.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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 method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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

#4: Protein 40S ribosomal protein S0 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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 , 17 types, 17 molecules CDFJKLNPRSTUXZfgq

#6: Protein KLLA0F09812p


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNI7
#45: Protein eIF3c,Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport ...eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport protein NIP1 / Translation initiation factor eIF3 / p93 subunit


Mass: 86539.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: NIP1, YMR309C, YM9924.01C, YM9952.11C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32497

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Protein/peptide , 1 types, 1 molecules h

#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 method: isolated from a natural source
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P0CX86

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

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


Mass: 17462.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38912
#39: Protein Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 34763.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20459
#40: Protein Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 57942.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: GCD11, TIF213, YER025W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32481
#41: Protein Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 31631.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SUI3, TIF212, YPL237W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P09064
#42: Protein Eukaryotic translation initiation factor 5 / eIF-5


Mass: 45321.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF5, YPR041W, YP3085.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38431
#43: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38249
#44: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PRT1, CDC63, YOR361C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P06103
#46: Protein Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF35, SCY_1313 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZZ25
#47: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 39 kDa subunit homolog / eIF-3 39 kDa subunit homolog


Mass: 38803.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF34, SCY_4321 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZMK5

+
Non-polymers , 4 types, 124 molecules

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


Mass: 24.305 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: Mg
#49: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#50: Chemical ChemComp-MET / METHIONINE / Methionine


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


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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 / 3D 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 C2)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
3tRNATransfer RNACOMPLEX11NATURAL
4initiation factorsInitiation factorCOMPLEX39,40,41,43,44,45,46,471RECOMBINANT
5initiation factorsInitiation factorCOMPLEX38,421RECOMBINANT
6mRNAMessenger RNACOMPLEX31RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)284590
23Saccharomyces cerevisiae (baker's yeast)4932
34Saccharomyces cerevisiae (baker's yeast)4932
45Saccharomyces cerevisiae (baker's yeast)4932
56Saccharomyces cerevisiae (baker's yeast)4932
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
14Saccharomyces cerevisiae (baker's yeast)4932
25Escherichia coli BL21(DE3) (bacteria)469008
36synthetic construct (others)32630
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 mMATPAdenosine triphosphate1
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 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2100
Details: Images were collected in movie-mode at 32 frames per second

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Processing

SoftwareName: REFMAC / Version: 5.8.0166 / Classification: refinement
EM software
IDNameVersionCategory
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 selectionNum. of particles selected: 394672
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157868 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 49 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: FSC
RefinementResolution: 3.05→268 Å / Cor.coef. Fo:Fc: 0.891 / SU B: 12.082 / SU ML: 0.202 / ESU R: 0.292
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.28889 --
Obs0.28889 1364807 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.43 Å20.33 Å2
2---0.57 Å2-0.16 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Total: 104243
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.016110873
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.1941.671157654
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg17.9978.22618481
ELECTRON MICROSCOPYr_dihedral_angle_2_deg43.0523.1752709
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.2581511353
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.38215541
ELECTRON MICROSCOPYr_chiral_restr0.1170.20717870
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02167484
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_it2.04814.22832494
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it3.69521.32540483
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.97911.02978379
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined9.059196831
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.576 100930 -
Rfree-0 -
Obs--100 %

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