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- PDB-3jap: Structure of a partial yeast 48S preinitiation complex in closed ... -

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Basic information

Entry
Database: PDB / ID: 3jap
TitleStructure of a partial yeast 48S preinitiation complex in closed conformation
Components
  • 18S rRNA
  • Met-tRNAi (U31:A39 variant)
  • RACK1
  • eIF1
  • eIF1A
  • eIF2 alpha
  • eIF2 beta
  • eIF2 gamma
  • eIF3a
  • eIF3b
  • eIF3c
  • eIF3g
  • eIF3i
  • eL41
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • mRNA
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsTRANSLATION / Eukaryotic translation initiation / 48S / small ribosome subunit / 40S / 43S
Function / homology
Function and homology information


formation of translation initiation ternary complex / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / eukaryotic translation initiation factor 3 complex, eIF3m / methionyl-initiator methionine tRNA binding / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 2 complex ...formation of translation initiation ternary complex / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / eukaryotic translation initiation factor 3 complex, eIF3m / methionyl-initiator methionine tRNA binding / incipient cellular bud site / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / 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 initiation factor binding / translation initiation factor activity / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / double-stranded RNA binding / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / SUI1 domain superfamily ...Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / Eukaryotic translation initiation factor eIF2A / SUI1 domain / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Eukaryotic translation initiation factor 3 subunit A / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S8e, conserved site
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / METHIONINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta / Small ribosomal subunit protein eS32A / Eukaryotic translation initiation factor 2 subunit alpha / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit gamma / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor eIF-1 / Small ribosomal subunit protein eS28 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 1A / Eukaryotic translation initiation factor 3 subunit I / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / KLLA0F09812p / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12277p / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / 40S ribosomal protein S3 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / Small ribosomal subunit protein uS8 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Kluyveromyces lactis (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsLlacer, J.L. / Hussain, T. / Ramakrishnan, V.
CitationJournal: Mol Cell / Year: 2015
Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.
Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan /
Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Other / Category: em_software / pdbx_database_status
Item: _em_software.image_processing_id / _em_software.name / _pdbx_database_status.pdb_format_compatible
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
1: Met-tRNAi (U31:A39 variant)
2: 18S rRNA
3: mRNA
A: uS2
B: eS1
C: uS5
D: uS3
E: eS4
F: uS7
G: eS6
H: eS7
I: eS8
J: uS4
K: eS10
L: uS17
M: eS12
N: uS15
O: uS11
P: uS19
Q: uS9
R: eS17
S: uS13
T: eS19
U: uS10
V: eS21
W: uS8
X: uS12
Y: eS24
Z: eS25
a: eS26
b: eS27
c: eS28
d: uS14
e: eS30
f: eS31
g: RACK1
h: eL41
i: eIF1A
j: eIF2 alpha
k: eIF2 gamma
l: eIF2 beta
m: eIF1
o: eIF3a
p: eIF3c
q: eIF3i
r: eIF3b
s: eIF3g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,546,901134
Polymers1,544,00147
Non-polymers2,90187
Water00
1


  • Idetical with deposited unit
  • defined by author
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 Met-tRNAi (U31:A39 variant)


Mass: 24223.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Kluyveromyces lactis (yeast)
#2: RNA chain 18S rRNA


Mass: 573814.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#3: RNA chain mRNA


Mass: 7786.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 42 types, 42 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#4: Protein uS2


Mass: 28264.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#5: Protein eS1


Mass: 28971.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#6: Protein uS5


Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#7: Protein uS3


Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#8: Protein eS4


Mass: 29617.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#9: Protein uS7


Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#10: Protein eS6


Mass: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#11: Protein eS7


Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#12: Protein eS8


Mass: 22642.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#13: Protein uS4


Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#14: Protein eS10


Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#15: Protein uS17


Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#16: Protein eS12


Mass: 14466.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#17: Protein uS15


Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#18: Protein uS11


Mass: 14530.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#19: Protein uS19


Mass: 15986.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#20: Protein uS9


Mass: 15874.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#21: Protein eS17


Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#22: Protein uS13


Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#23: Protein eS19


Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#24: Protein uS10


Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#25: Protein eS21


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#26: Protein uS8


Mass: 14645.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#27: Protein uS12


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: F2Z602
#28: Protein eS24


Mass: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#29: Protein eS25


Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#30: Protein eS26


Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#31: Protein eS27


Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#32: Protein eS28


Mass: 7549.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#33: Protein uS14


Mass: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#34: Protein eS30


Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#35: Protein eS31


Mass: 17110.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#36: Protein RACK1


Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#38: Protein eIF1A


Mass: 17462.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pTYB2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P38912
#39: Protein eIF2 alpha


Mass: 34763.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20459
#40: Protein eIF2 gamma


Mass: 57942.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32481
#41: Protein eIF2 beta


Mass: 31631.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09064
#42: Protein eIF1


Mass: 12330.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pTYB2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta / References: UniProt: P32911
#43: Protein eIF3a


Mass: 64752.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38249
#44: Protein eIF3c


Mass: 73397.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32497
#45: Protein eIF3i


Mass: 38803.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40217
#47: Protein eIF3g


Mass: 5942.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A6ZZ25

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Protein/peptide , 2 types, 2 molecules hr

#37: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P0CX86
#46: Protein/peptide eIF3b


Mass: 3963.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06103

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Non-polymers , 4 types, 87 molecules

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


Mass: 24.305 Da / Num. of mol.: 81 / Source method: obtained synthetically / Formula: Mg
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#50: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / 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
IDNameTypeParent-ID
1Partial yeast 48S preinitiation complexRIBOSOME0
240S ribosomeRIBOSOME1
3Eukaryotic initiation factor eIF1A1
4Eukaryotic initiation factor eIF21
5Eukaryotic initiation factor eIF11
6Eukaryotic initiation factor eIF31
7Met-tRNAi1
8mRNA1
Buffer solutionName: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
pH: 6.5
Details: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 %
Details: Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I).
Method: Blot for 2.5 to 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 4, 2014
Details: Complete dataset was collected over two non-consecutive days.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 5500
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0124 2015/06/03 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameCategory
1Cootmodel fitting
2REFMACmodel fitting
3UCSF Chimeramodel fitting
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21401 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Details: gold-standard / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor, FSC / Details: METHOD--Local refinement
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13J81

3j81

13J811PDBexperimental model
23CW2

3cw2

13CW22PDBexperimental model
32D74

2d74

12D743PDBexperimental model
44U1C

4u1c

14U1C4PDBexperimental model
54U1D

4u1d

14U1D5PDBexperimental model
64U1E

4u1e

14U1E6PDBexperimental model
RefinementDetails: Hydrogens have been added in their riding positions
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms58517 39691 125 0 98333

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