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- PDB-6yam: Mammalian 48S late-stage translation initiation complex (LS48S+eI... -

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Basic information

Entry
Database: PDB / ID: 6yam
TitleMammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNA
Components
  • (40S ribosomal protein ...) x 27
  • (Eukaryotic translation initiation factor 3 subunit ...) x 9
  • (eukaryotic translation initiation factor 2 subunit ...) x 2
  • (ribosomal protein ...) x 6
  • 18S ribosomal RNA
  • 60s ribosomal protein l41
  • ATP-binding cassette sub-family E member 1 (ABCE1)
  • beta-globin mRNA
  • eukaryotic translation initiation factor 1A
  • initiator methionylated tRNA
KeywordsTRANSLATION / translation initiation / eukaryotic initiation factor 1 / eukaryotic initiation factor 1A / eukaryotic initiation factor 3 / late-stage initiation complex / rabbit
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / ribosomal subunit / metal-dependent deubiquitinase activity / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / regulation of translational fidelity / ribosomal small subunit export from nucleus / laminin binding / rough endoplasmic reticulum / translation regulator activity / translation initiation factor binding / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / positive regulation of translation / maturation of SSU-rRNA / small-subunit processome / PML body / spindle / cytoplasmic stress granule / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / perikaryon / cysteine-type deubiquitinase activity / cytoplasmic translation / cell differentiation / mitochondrial inner membrane / postsynaptic density / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / synapse / centrosome / dendrite / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K ...Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit 6 N terminal domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / : / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / 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 / 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 / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / JAB/MPN domain / Ribosomal protein S7e / Ribosomal protein S7e / JAB1/MPN/MOV34 metalloenzyme domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19A/S15e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Eukaryotic translation initiation factor 3 subunit A / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Eukaryotic translation initiation factor 3 subunit A / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / Small ribosomal subunit protein uS15 / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 3 subunit K / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 3 subunit C / Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBochler, A. / Simonetti, A. / Guca, E. / Hashem, Y.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Research Council (ERC)759120European Union
French National Research AgencyANR-14-ACHN-0024 France
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Authors: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem /
Abstract: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
History
DepositionMar 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
1: initiator methionylated tRNA
l: 60s ribosomal protein l41
C: 40S ribosomal protein uS2
D: 40S ribosomal protein eS1
E: 40S ribosomal protein uS5
F: 40S ribosomal protein uS3
G: 40S ribosomal protein eS4
H: 40S ribosomal protein uS7
I: 40S ribosomal protein eS6
J: ribosomal protein eS7
K: 40S ribosomal protein eS8
L: 40S ribosomal protein uS4
M: 40S ribosomal protein eS10
N: 40S ribosomal protein uS17
O: 40S ribosomal protein eS12
P: ribosomal protein uS15
Q: 40S ribosomal protein uS11
S: 40S ribosomal protein uS9
T: 40S ribosomal protein eS17
V: 40S ribosomal protein eS19
W: 40S ribosomal protein uS10
X: 40S ribosomal protein eS21
Y: 40S ribosomal protein uS8
Z: 40S ribosomal protein uS12
a: 40S ribosomal protein eS24
b: 40S ribosomal protein eS26
c: 40S ribosomal protein eS27
d: 40S ribosomal protein eS28
e: ribosomal protein uS14
f: ribosomal protein eS31
g: ribosomal protein RACK1
n: ribosomal protein eS25
i: 40S ribosomal protein eS30
2: 18S ribosomal RNA
A: eukaryotic translation initiation factor 2 subunit alpha
B: eukaryotic translation initiation factor 2 subunit gamma
j: eukaryotic translation initiation factor 1A
k: ATP-binding cassette sub-family E member 1 (ABCE1)
U: 40S ribosomal protein uS13
R: 40S ribosomal protein uS19
3: beta-globin mRNA
m: eukaryotic translation initiation factor 3 subunit d
y: Eukaryotic translation initiation factor 3 subunit A
v: Eukaryotic translation initiation factor 3 subunit C
w: Eukaryotic translation initiation factor 3 subunit E
q: Eukaryotic translation initiation factor 3 subunit F
r: eukaryotic translation initiation factor 3 subunit h
s: Eukaryotic translation initiation factor 3 subunit K
t: eukaryotic translation initiation factor 3 subunit l
u: Eukaryotic translation initiation factor 3 subunit M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,967,71755
Polymers1,965,94550
Non-polymers1,7725
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain initiator methionylated tRNA


Mass: 24376.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A at position 37 is modified (threonyl-carbamoyl-adenosine (t6A))
Source: (natural) Oryctolagus cuniculus (rabbit)
#34: RNA chain 18S ribosomal RNA


Mass: 601015.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: U at position 1244 is modified / Source: (natural) Oryctolagus cuniculus (rabbit)
#41: RNA chain beta-globin mRNA


Mass: 14454.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein/peptide , 1 types, 1 molecules l

#2: Protein/peptide 60s ribosomal protein l41 / eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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40S ribosomal protein ... , 27 types, 27 molecules CDEFGHIKLMNOQSTVWXYZabcdiUR

#3: Protein 40S ribosomal protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 23360.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#4: Protein 40S ribosomal protein eS1


Mass: 29928.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN72
#5: Protein 40S ribosomal protein uS5


Mass: 24814.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#6: Protein 40S ribosomal protein uS3


Mass: 25158.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#7: Protein 40S ribosomal protein eS4


Mass: 29658.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#8: Protein 40S ribosomal protein uS7


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KMN4
#9: Protein 40S ribosomal protein eS6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#11: Protein 40S ribosomal protein eS8


Mass: 23902.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#12: Protein 40S ribosomal protein uS4


Mass: 21266.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#13: Protein 40S ribosomal protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T168
#14: Protein 40S ribosomal protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#15: Protein 40S ribosomal protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#17: Protein 40S ribosomal protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#18: Protein 40S ribosomal protein uS9


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#19: Protein 40S ribosomal protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein 40S ribosomal protein eS19


Mass: 16235.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#21: Protein 40S ribosomal protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#22: Protein 40S ribosomal protein eS21


Mass: 8896.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#23: Protein 40S ribosomal protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#24: Protein 40S ribosomal protein uS12


Mass: 15757.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#25: Protein 40S ribosomal protein eS24


Mass: 15434.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TS40
#26: Protein 40S ribosomal protein eS26


Mass: 12961.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#27: Protein 40S ribosomal protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#28: Protein 40S ribosomal protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#33: Protein 40S ribosomal protein eS30


Mass: 6741.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#39: Protein 40S ribosomal protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#40: Protein 40S ribosomal protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2

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Ribosomal protein ... , 6 types, 6 molecules JPefgn

#10: Protein ribosomal protein eS7


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#16: Protein ribosomal protein uS15


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#29: Protein ribosomal protein uS14


Mass: 6364.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#30: Protein ribosomal protein eS31


Mass: 8358.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#31: Protein ribosomal protein RACK1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#32: Protein ribosomal protein eS25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3

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Eukaryotic translation initiation factor 2 subunit ... , 2 types, 2 molecules AB

#35: Protein eukaryotic translation initiation factor 2 subunit alpha


Mass: 30633.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4
#36: Protein eukaryotic translation initiation factor 2 subunit gamma


Mass: 45862.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 2 types, 2 molecules jk

#37: Protein eukaryotic translation initiation factor 1A


Mass: 16488.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: Protein ATP-binding cassette sub-family E member 1 (ABCE1)


Mass: 66986.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Eukaryotic translation initiation factor 3 subunit ... , 9 types, 9 molecules myvwqrstu

#42: Protein eukaryotic translation initiation factor 3 subunit d


Mass: 64042.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#43: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta


Mass: 163226.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9C991
#44: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105676.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U971
#45: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / eIF-3 p48


Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SUC8
#46: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 30111.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SLC2
#47: Protein eukaryotic translation initiation factor 3 subunit h


Mass: 39954.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#48: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / eIF-3 p25


Mass: 25129.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3L2
#49: Protein eukaryotic translation initiation factor 3 subunit l


Mass: 66776.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SLW8

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Non-polymers , 3 types, 5 molecules

#51: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#52: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#53: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN
Has protein modificationY

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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
1LS48S+eIF3 IC with beta-globin mRNACOMPLEX#1-#40, #42-#500MULTIPLE SOURCES
2LS48S+eIF3 ICRIBOSOME#1-#501NATURAL
3beta-globin mRNACOMPLEX#411RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Homo sapiens (human)9606
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 26 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43450 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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