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- PDB-8i7j: Yeast 40S-eIF4B - partially open conformation of the 40S head -

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Basic information

Entry
Database: PDB / ID: 8i7j
TitleYeast 40S-eIF4B - partially open conformation of the 40S head
Components
  • (40S ribosomal protein ...) x 17
  • 60S ribosomal protein L41-A
  • KLLA0A07194p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B07931p
  • KLLA0B08173p
  • KLLA0B11231p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0E12277p
  • KLLA0E23673p
  • KLLA0F07843p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F25542p
  • RNA (1780-MER)
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME
Function / homology
Function and homology information


GDP-dissociation inhibitor activity / 90S preribosome / ribosomal subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome ...GDP-dissociation inhibitor activity / 90S preribosome / ribosomal subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily ...: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal protein S7e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S27e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S8e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / KLLA0B11231p / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS10 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / KLLA0B11231p / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS10 / KLLA0F18040p / Small ribosomal subunit protein uS5 / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / RP21 / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein RACK1 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / Small ribosomal subunit protein uS3 / 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 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / RP41 / S16a / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Kluyveromyces lactis NRRL Y-1140 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsDatey, A. / Khaja, F.T. / Hussain, T.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/I/17/2/503313 India
CitationJournal: Biochemistry / Year: 2025
Title: Yeast Eukaryotic Initiation Factor 4B Remodels the MRNA Entry Site on the Small Ribosomal Subunit.
Authors: Ayushi Datey / Prafful Sharma / Faisal Tarique Khaja / Huma Rahil / Tanweer Hussain /
Abstract: Eukaryotic Initiation Factor 4 (eIF4) is a group of factors that activates mRNA for translation and recruit 43S preinitiation complex (PIC) to the mRNA 5' end, forming the 48S PIC. The eIF4 factors ...Eukaryotic Initiation Factor 4 (eIF4) is a group of factors that activates mRNA for translation and recruit 43S preinitiation complex (PIC) to the mRNA 5' end, forming the 48S PIC. The eIF4 factors include mRNA 5' cap-binding protein eIF4E, ATP-dependent RNA helicase eIF4A, and scaffold protein eIF4G, which anchors eIF4A and eIF4E. Another eIF4 factor, eIF4B, stimulates the RNA helicase activity of eIF4A and facilitates mRNA recruitment. However, the mechanisms by which eIF4B binds the 40S ribosomal subunit and promotes mRNA recruitment remain poorly understood. Using cryo-Eletron Microscopy (cryo-EM), we obtained a map of the yeast 40S ribosomal subunit in a complex with eIF4B (40S-eIF4B complex). An extra density, tentatively assigned to yeast eIF4B, was observed near the mRNA entry channel of the 40S, contacting ribosomal proteins uS10, uS3, and eS10 as well as rRNA helix h16. Predictive modeling of the 40S-eIF4B complex suggests that the N-terminal domain of eIF4B binds near the mRNA entry channel, overlapping with the extra density observed in the 40S-eIF4B map. The partially open conformation of 40S in the 40S-eIF4B map is incompatible with eIF3j binding observed in the 48S PIC. Additionally, the extra density at the mRNA entry channel poses steric hindrance for eIF3g binding in the 48S PIC. Thus, structural insights suggest that eIF4B facilitates the release of eIF3j and the relocation of the eIF3b-g-i module during mRNA recruitment, thereby advancing our understanding of eIF4B's role in translation initiation.
History
DepositionJan 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: RNA (1780-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: KLLA0B07931p
X: KLLA0B11231p
Y: 40S ribosomal protein S24
Z: 40S ribosomal protein S25
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,176,97840
Polymers1,176,73335
Non-polymers2455
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The evidence of the assembly has been reported in earlier studies published by Walker et al., in 2013.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#2: Protein 40S ribosomal protein S0


Mass: 28264.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CN12
#3: Protein 40S ribosomal protein S1


Mass: 28971.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWD0
#6: Protein 40S ribosomal protein S4


Mass: 29617.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWJ2
#8: Protein 40S ribosomal protein S6


Mass: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CM04
#9: Protein 40S ribosomal protein S7


Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CTD6
#10: Protein 40S ribosomal protein S8


Mass: 22642.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CMG3
#14: Protein 40S ribosomal protein S12


Mass: 14466.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CLU4
#16: 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 NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: P27069
#18: Protein 40S ribosomal protein S16


Mass: 15874.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q875N2
#23: Protein 40S ribosomal protein S21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CXT6
#26: Protein 40S ribosomal protein S24


Mass: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CU44
#27: Protein 40S ribosomal protein S25


Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CW78
#28: Protein 40S ribosomal protein S26


Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CS01
#29: Protein 40S ribosomal protein S27


Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CNL2
#30: 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 NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: P33285
#31: Protein 40S ribosomal protein S29


Mass: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CPG3
#32: Protein 40S ribosomal protein S30


Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CUH5

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Protein , 16 types, 16 molecules CDFJKLNPRSTUWXfg

#4: Protein KLLA0F09812p


Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CKL3
#5: Protein KLLA0D08305p


Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CRK7
#7: Protein KLLA0D10659p


Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CRA3
#11: Protein KLLA0E23673p


Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CM18
#12: Protein KLLA0B08173p


Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CVZ5
#13: Protein KLLA0A10483p


Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CX80
#15: Protein KLLA0F18040p


Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CJK0
#17: Protein KLLA0F07843p


Mass: 15986.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CKV4
#19: Protein KLLA0B01474p


Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWU3
#20: Protein KLLA0B01562p


Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CWT9
#21: Protein KLLA0A07194p


Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CXM0
#22: Protein KLLA0F25542p


Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CIM1
#24: Protein KLLA0B07931p


Mass: 14645.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CW06
#25: Protein KLLA0B11231p


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: F2Z602
#33: 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 NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: P69061
#34: Protein KLLA0E12277p


Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140 / References: UniProt: Q6CNI7

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RNA chain / Protein/peptide , 2 types, 2 molecules 2h

#1: RNA chain RNA (1780-MER)


Mass: 579545.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis NRRL Y-1140 (yeast) / Strain: NRRL Y-1140
#35: Protein/peptide 60S ribosomal protein L41-A / L47 / Large ribosomal subunit protein eL41-A / YL41


Mass: 3354.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: RPL41A / Production host: Escherichia coli (E. coli) / References: UniProt: P0CX86

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Non-polymers , 2 types, 5 molecules

#36: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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
IDNameTypeDetailsEntity IDParent-IDSource
1The binary complex of the yeast 40S small ribosomal subunit with the eukaryotic initiation factor 4B.RIBOSOME40S purified from Kluyveromyces lactis and Saccharomyces cerevisiae eIF4B overexpressed and purified from Escherichia coli#1-#350MULTIPLE SOURCES
2Eukaryotic Initiation Factor 4B (eIF4B).COMPLEXeIF4B is a part of the binary complex along with the 40S ribosomal subunit. eIF4B is present and associated with the 40S near its mRNA channel entry site on the solvent-exposed side. The Saccharomyces cerevisiae eIF4B was recombinantly expressed and purified from the E. coli expression system.#351RECOMBINANT
3yeast 40S small ribosomal subunitCOMPLEX#1-#341NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)

Cellular location: cytoplasm

IDEntity assembly-IDOrganismNcbi tax-IDStrainTissueOrganOrganelle
21Saccharomyces cerevisiae S288c (yeast)559292S288cSingle cell yeast
32Kluyveromyces lactis Saccharomyces cerevisiae S288c (yeast)28985NRRL Y-1140yeastyeastribosome
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta(DE3)pLysS / Plasmid: pTYB2
Buffer solutionpH: 7.4
Details: 20 mM HEPES pH7.4, 100 mM potassium acetate pH7.6, 2.5 mM Magnesium acetate, 2 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMPotassium acetateCH3CO2K1
32.5 mMMagnesium acetateC2H6O4Mg1
42 mMDithiothreitolC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This class of empty or only 40S was a part of the reaction mixture containing 40S and the Saccharomyces cerevisiae eukaryotic initiation factor 4B present in a 1:10 molar ratio
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Vitrification was carried out in nitrogen atmosphere.

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Details: Preliminary grid screening was done manually using the Latitude-S
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal magnification: 42000 X / Calibrated magnification: 42000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN / Temperature (max): 98 K / Temperature (min): 77 K
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 6 / Num. of real images: 7975
Details: Images were collected in movie-mode at 20 frames in 8 seconds
Image scansMovie frames/image: 20 / Used frames/image: 4-16

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Processing

EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2LatitudeSimage acquisition
4RELION3.1.1CTF correction
7UCSF Chimera1.15model fitting
9RELION3.1.1initial Euler assignment
10RELION3.1.1final Euler assignment
12RELION3.1.13D reconstruction
13PHENIX1.18.2-3874model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1492547
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108616 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00681414
ELECTRON MICROSCOPYf_angle_d0.964118539
ELECTRON MICROSCOPYf_dihedral_angle_d22.58426729
ELECTRON MICROSCOPYf_chiral_restr0.05114812
ELECTRON MICROSCOPYf_plane_restr0.0068500

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