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Entry
Database: PDB / ID: 6swe
TitleIC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Components
  • (30S ribosomal protein ...) x 11
  • 16S ribosomal RNA
  • 50S ribosomal protein L7Ae
  • Translation initiation factor 1A
  • initiator Met-tRNA fMet from E. coli (A1U72 variant)
KeywordsRIBOSOME / Translation initiation / cryo-EM / tRNA / evolution / archaea / rRNA modifications
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S17 / Ribosomal protein S27ae / Diphtheria Toxin Repressor; domain 2 / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S3, archaeal / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S14, type Z, archaeal / Translation initiation factor 1A (eIF-1A), conserved site ...Ribosomal protein S17 / Ribosomal protein S27ae / Diphtheria Toxin Repressor; domain 2 / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S3, archaeal / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S14, type Z, archaeal / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal protein S10 / Ribosomal Protein S7 / Ribosomal protein S7/S5 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal protein L30/S12 / Ribosomal protein L7Ae, archaea / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Nucleic acid-binding proteins / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Few Secondary Structures / Irregular / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 ...RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Translation initiation factor 1A / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCoureux, P.-D. / Mechulam, Y. / Schmitt, E.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0037 France
CitationJournal: Commun Biol / Year: 2020
Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /
Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 19, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
2: 16S ribosomal RNA
H: 30S ribosomal protein S7
K: 30S ribosomal protein S9
L: 30S ribosomal protein S10
O: 30S ribosomal protein S13
P: 30S ribosomal protein S14 type Z
S: 30S ribosomal protein S17e
T: 30S ribosomal protein S19
U: 30S ribosomal protein S19e
X: 30S ribosomal protein S28e
Y: 30S ribosomal protein S27ae
Z: 30S ribosomal protein S3
3: 50S ribosomal protein L7Ae
4: initiator Met-tRNA fMet from E. coli (A1U72 variant)
6: Translation initiation factor 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,35724
Polymers338,09715
Non-polymers2609
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area64330 Å2
ΔGint-510 kcal/mol
Surface area126660 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules 24

#1: RNA chain 16S ribosomal RNA


Mass: 152069.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)
#14: RNA chain initiator Met-tRNA fMet from E. coli (A1U72 variant)


Mass: 5761.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Variant: A1U72 / Production host: Escherichia coli (E. coli)

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30S ribosomal protein ... , 11 types, 11 molecules HKLOPSTUXYZ

#2: Protein 30S ribosomal protein S7


Mass: 24662.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V109
#3: Protein 30S ribosomal protein S9


Mass: 15293.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V195
#4: Protein 30S ribosomal protein S10


Mass: 11795.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V0V6
#5: Protein 30S ribosomal protein S13


Mass: 16992.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1A0
#6: Protein 30S ribosomal protein S14 type Z


Mass: 6644.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P62012
#7: Protein 30S ribosomal protein S17e


Mass: 8059.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V0G0
#8: Protein 30S ribosomal protein S19


Mass: 15307.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1T9
#9: Protein 30S ribosomal protein S19e


Mass: 17422.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V0G8
#10: Protein 30S ribosomal protein S28e


Mass: 8102.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P61029
#11: Protein 30S ribosomal protein S27ae


Mass: 5992.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P61238
#12: Protein 30S ribosomal protein S3


Mass: 23472.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: Q9V1U1

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Protein , 2 types, 2 molecules 36

#13: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13442.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / References: UniProt: P62008
#15: Protein Translation initiation factor 1A / aIF-1A


Mass: 13078.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: eIF1A, aif1A, PYRAB05910, PAB2441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V138

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Non-polymers , 3 types, 27 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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
1Archaeal translation initiation complex devoid of aIF1 - IC2 headRIBOSOME#1-#150MULTIPLE SOURCES
230SCOMPLEX#1-#131NATURAL
3initiator Met-tRNA fMet from E. coli (A1U72 variant)COMPLEX#141RECOMBINANT
4translation initiation factor 1ACOMPLEX#151RECOMBINANT
Molecular weightValue: 1.05 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pyrococcus abyssi (strain GE5 / Orsay) (archaea)272844
23Escherichia coli (E. coli)562
34Pyrococcus abyssi (strain GE5 / Orsay) (archaea)272844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24Escherichia coli (E. coli)562
Buffer solutionpH: 6.7
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: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0124197
ELECTRON MICROSCOPYf_angle_d0.90235009
ELECTRON MICROSCOPYf_dihedral_angle_d11.2313574
ELECTRON MICROSCOPYf_chiral_restr0.0554244
ELECTRON MICROSCOPYf_plane_restr0.0062641

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