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- PDB-6ybs: Structure of a human 48S translational initiation complex - head -

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Database: PDB / ID: 6ybs
TitleStructure of a human 48S translational initiation complex - head
Components
  • (40S ribosomal protein ...) x 13
  • (Eukaryotic translation initiation factor 3 subunit ...) x 2
  • 18S rRNA18S ribosomal RNA
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsTRANSLATION / 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, eIF3m / positive regulation of mRNA binding / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / negative regulation of DNA repair / positive regulation of base-excision repair / oxidized pyrimidine DNA binding ...mRNA cap binding / cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / positive regulation of mRNA binding / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / negative regulation of DNA repair / positive regulation of base-excision repair / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of DNA N-glycosylase activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / eukaryotic 43S preinitiation complex / nucleolus organization / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / response to extracellular stimulus / NF-kappaB complex / positive regulation of Golgi to plasma membrane protein transport / IRE1-RACK1-PP2A complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of endodeoxyribonuclease activity / regulation of cell division / oxidized purine DNA binding / negative regulation of endoplasmic reticulum unfolded protein response / protein kinase A binding / supercoiled DNA binding / negative regulation of hydrogen peroxide-induced neuron death / positive regulation of ceramide biosynthetic process / signaling adaptor activity / erythrocyte homeostasis / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of Wnt signaling pathway / pigmentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of T cell receptor signaling pathway / positive regulation of mitochondrial depolarization / phagocytic cup / rescue of stalled ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / positive regulation of cellular component movement / fibroblast growth factor binding / iron-sulfur cluster binding / ion channel inhibitor activity / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / monocyte chemotaxis / positive regulation of interleukin-2 production / BH3 domain binding / positive regulation of cyclic-nucleotide phosphodiesterase activity / spindle assembly / ribosomal small subunit export from nucleus / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of JUN kinase activity / negative regulation of protein kinase B signaling / SRP-dependent cotranslational protein targeting to membrane / maturation of SSU-rRNA / regulation of translational fidelity / gastrulation / negative regulation of respiratory burst involved in inflammatory response / polysome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ribosomal small subunit biogenesis / viral transcription / positive regulation of DNA repair / molecular adaptor activity / Hsp70 protein binding / erythrocyte differentiation / tubulin binding / translation initiation factor activity / translational initiation / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / MyD88-independent toll-like receptor signaling pathway / polysomal ribosome / osteoblast differentiation / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / SH2 domain binding / cyclin binding / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / mitotic spindle / global genome nucleotide-excision repair / chromosome segregation / host cell / nucleotide-excision repair, preincision complex assembly
Ribosomal protein S27a / Ribosomal protein S10, conserved site / Ribosomal protein S17e / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Eukaryotic translation initiation factor 3 subunit G / WD40-repeat-containing domain / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S13, conserved site ...Ribosomal protein S27a / Ribosomal protein S10, conserved site / Ribosomal protein S17e / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Eukaryotic translation initiation factor 3 subunit G / WD40-repeat-containing domain / Ribosomal protein S14 / Ribosomal protein S9 / Ribosomal protein S13, conserved site / Ribosomal protein S19e / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin-like domain / Ribosomal protein S5 domain 2-type fold, subgroup / Nucleotide-binding alpha-beta plait domain superfamily / G-protein beta WD-40 repeat / Ribosomal protein S13 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain, type 2 / Ribosomal protein S25 / Plectin/S10, N-terminal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S10 / Nucleic acid-binding, OB-fold / Ribosomal protein S10, eukaryotic/archaeal / WD40 repeat / Eukaryotic translation initiation factor 3 subunit D / K homology domain superfamily, prokaryotic type / Ribosomal protein S3, C-terminal / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Ribosomal protein S19/S15 / Ubiquitin domain / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S7 domain superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S9, conserved site / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S28e / Ribosomal protein S5/S7 / Ribosomal protein S12e / Ribosomal protein S10 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / S27a-like superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S14/S29 / RNA recognition motif domain / Winged helix DNA-binding domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S10 domain / Ribosomal protein S19 conserved site / RNA-binding domain superfamily / Ribosomal protein S7, conserved site / Eukaryotic translation initiation factor 3 subunit G, N-terminal / 30s ribosomal protein S13, C-terminal / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / eIF3G, RNA recognition motif / Ribosomal protein S19, superfamily
40S ribosomal protein S16 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S28 / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / 40S ribosomal protein S20 / Eukaryotic translation initiation factor 3 subunit D / 40S ribosomal protein S10 ...40S ribosomal protein S16 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S28 / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / 40S ribosomal protein S20 / Eukaryotic translation initiation factor 3 subunit D / 40S ribosomal protein S10 / 40S ribosomal protein S5 / 40S ribosomal protein S19 / 40S ribosomal protein S12 / 40S ribosomal protein S3 / 40S ribosomal protein S17 / Eukaryotic translation initiation factor 3 subunit G / Receptor of activated protein C kinase 1
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
x: Eukaryotic translation initiation factor 3 subunit D
c: Receptor of activated protein C kinase 1
n: 40S ribosomal protein S28
X: 40S ribosomal protein S17
h: 40S ribosomal protein S20
o: Eukaryotic translation initiation factor 3 subunit G
a: 40S ribosomal protein S10
m: 40S ribosomal protein S12
i: 40S ribosomal protein S29
b: 40S ribosomal protein S15
Z: 40S ribosomal protein S3
d: 40S ribosomal protein S19
e: 40S ribosomal protein S25
f: 40S ribosomal protein S18
V: 40S ribosomal protein S5
k: Ubiquitin-40S ribosomal protein S27a
Y: 40S ribosomal protein S16
A: 18S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)965,67048
Polymers964,90018
Non-polymers77030
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Eukaryotic translation initiation factor 3 subunit ... , 2 types, 2 molecules xo

#1: 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
#6: Protein Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75821

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Protein , 2 types, 2 molecules ck

#2: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#16: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

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40S ribosomal protein ... , 13 types, 13 molecules nXhamibZdefVY

#3: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#4: 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
#5: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#7: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#8: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#9: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#10: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#11: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#12: Protein 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#13: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#14: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#15: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#17: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249

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RNA chain , 1 types, 1 molecules A

#18: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 604237.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 2 types, 30 molecules

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


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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-#18 / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144882 / Symmetry type: POINT

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