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- PDB-6ybd: Structure of a human 48S translational initiation complex - eIF3 -

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Entry
Database: PDB / ID: 6ybd
TitleStructure of a human 48S translational initiation complex - eIF3
Components
  • (40S ribosomal protein ...) x 10
  • (Eukaryotic translation initiation factor 3 subunit ...) x 9
KeywordsTRANSLATION / eIF3 / ribosome / initiation complex
Function / homology
Function and homology information


mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / positive regulation of mRNA binding / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation ...mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / positive regulation of mRNA binding / IRES-dependent viral translational initiation / multi-eIF complex / cytoplasmic translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / negative regulation of RNA splicing / eukaryotic 48S preinitiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / formation of cytoplasmic translation initiation complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / regulation of translational initiation / erythrocyte homeostasis / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / fibroblast growth factor binding / poly(U) RNA binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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) / positive regulation of ubiquitin-protein transferase activity / SRP-dependent cotranslational protein targeting to membrane / maturation of SSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of translational initiation / ribosomal small subunit biogenesis / translation initiation factor binding / viral transcription / thiol-dependent ubiquitin-specific protease activity / erythrocyte differentiation / laminin binding / translation initiation factor activity / translational initiation / polysomal ribosome / mRNA 3'-UTR binding / rough endoplasmic reticulum / microtubule organizing center / negative regulation of ERK1 and ERK2 cascade / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / metallopeptidase activity / positive regulation of translation / fibrillar center / neural tube closure / mRNA 5'-UTR binding / ubiquitinyl hydrolase 1 / rRNA processing / receptor tyrosine kinase binding / PML body / cytoplasmic translation / virus receptor activity / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / ribonucleoprotein complex / protein N-terminus binding / microtubule / protein stabilization / ribosome / structural constituent of ribosome / cell differentiation / postsynaptic density / protein deubiquitination / translation / cadherin binding / cell adhesion / mRNA binding / synapse / focal adhesion / nucleolus / positive regulation of gene expression / structural molecule activity / viral process / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / RNA binding / DNA binding / extracellular exosome / zinc ion binding / membrane / nucleoplasm / plasma membrane / nucleus / cytosol / cytoplasm
Ribosomal protein S5, C-terminal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Armadillo-type fold / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S2, conserved site / Zinc-binding ribosomal protein ...Ribosomal protein S5, C-terminal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein S5 domain 2-type fold, subgroup / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Armadillo-type fold / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S2, conserved site / Zinc-binding ribosomal protein / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Translation initiation factor 3 complex subunit L / Ribosomal protein S5 domain 2-type fold / Tetratricopeptide-like helical domain superfamily / Eukaryotic translation initiation factor 3 subunit K / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S5 / Ribosomal protein S11 / Ribosomal protein S21e / Ribosomal protein S2 / Ribosomal protein S3Ae / Ribosomal protein S17e / Ribosomal protein S26e / Proteasome component (PCI) domain / S15/NS1, RNA-binding / Ribosomal protein S27e / Ribosomal protein S15 / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S7e / Ribosomal protein S5, eukaryotic/archaeal / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Ribosomal protein S15P / Ribosomal S11, conserved site / Rpn11/EIF3F, C-terminal / Winged helix-like DNA-binding domain superfamily / 40S ribosomal protein SA, C-terminal domain / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit M / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Eukaryotic translation initiation factor 3 subunit H / Ribosomal protein S11 superfamily / MPN domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S26e superfamily / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / eIF3 subunit M, C-terminal helix domain / CSN8/PSMD8/EIF3K
Eukaryotic translation initiation factor 3 subunit F / 40S ribosomal protein S14 / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S21 / 40S ribosomal protein S26 / 40S ribosomal protein S13 / 40S ribosomal protein S7 ...Eukaryotic translation initiation factor 3 subunit F / 40S ribosomal protein S14 / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S21 / 40S ribosomal protein S26 / 40S ribosomal protein S13 / 40S ribosomal protein S7 / Eukaryotic translation initiation factor 3 subunit D / 40S ribosomal protein S3a / Eukaryotic translation initiation factor 3 subunit E / 40S ribosomal protein S27 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S17 / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit L
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBrito Querido, J. / Sokabe, M. / Kraatz, S. / Gordiyenko, Y. / Skehel, M. / Fraser, C. / Ramakrishnan, V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
6: Eukaryotic translation initiation factor 3 subunit M
4: Eukaryotic translation initiation factor 3 subunit F
u: Eukaryotic translation initiation factor 3 subunit A
v: Eukaryotic translation initiation factor 3 subunit E
y: Eukaryotic translation initiation factor 3 subunit C
8: Eukaryotic translation initiation factor 3 subunit H
G: 40S ribosomal protein S7
H: 40S ribosomal protein S27
K: 40S ribosomal protein S21
M: 40S ribosomal protein S17
L: 40S ribosomal protein S2
O: 40S ribosomal protein S3a
N: 40S ribosomal protein SA
Q: 40S ribosomal protein S26
P: 40S ribosomal protein S14
I: 40S ribosomal protein S13
x: Eukaryotic translation initiation factor 3 subunit D
3: Eukaryotic translation initiation factor 3 subunit K
5: Eukaryotic translation initiation factor 3 subunit L


Theoretical massNumber of molelcules
Total (without water)797,99019
Polymers797,99019
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Eukaryotic translation initiation factor 3 subunit ... , 9 types, 9 molecules 64uvy8x35

#1: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7L2H7
#2: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00303, ubiquitinyl hydrolase 1
#3: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


Mass: 166903.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14152
#4: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 ...eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60228
#5: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99613
#6: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15372
#17: Protein Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15371
#18: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBQ5
#19: Protein Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y262

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40S ribosomal protein ... , 10 types, 10 molecules GHKMLONQPI

#7: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#8: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#9: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#10: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#11: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#12: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#13: Protein 40S ribosomal protein SA / / 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 / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#14: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#15: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#16: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277

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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

ComponentName: 48S initiation complex / Type: RIBOSOME / Entity ID: #1-#19 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy
Image recordingAverage exposure time: 1 sec. / Electron dose: 107 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11882 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 142.13 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008431150
ELECTRON MICROSCOPYf_angle_d1.023742338
ELECTRON MICROSCOPYf_chiral_restr0.05965043
ELECTRON MICROSCOPYf_plane_restr0.00735595
ELECTRON MICROSCOPYf_dihedral_angle_d22.66334683

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