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- PDB-6swd: IC2 body model of cryo-EM structure of a full archaeal ribosomal ... -

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Basic information

Entry
Database: PDB / ID: 6swd
TitleIC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Components
  • (30S ribosomal protein ...) x 15
  • 16S ribosomal RNA
  • Translation initiation factor 1A
  • Zn-ribbon RNA-binding protein involved in translation
  • mRNAMessenger RNA
KeywordsRIBOSOME / Translation initiation / cryo-EM / tRNA / evolution / archaea / rRNA modifications
Function / homology
Function and homology information


translation initiation factor activity / cytosolic ribosome / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding
Similarity search - Function
Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27 / : / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / 30S ribosomal protein S3Ae ...Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Small zinc finger protein HVO_2753-like, Zn-binding pocket / Ribosomal protein S27 / : / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / 30S ribosomal protein S3Ae / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S8e, 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) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / S15/NS1, RNA-binding / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / N-terminal domain of TfIIb / Ribosomal protein S3Ae, conserved site / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal family S4e / Ribosomal S13/S15 N-terminal domain / RRM (RNA recognition motif) domain / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Ribosomal protein S2 signature 2. / : / Ribosomal protein S17, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / Ribosomal protein S11 / RNA-binding S4 domain
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS27 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS8 / Translation initiation factor 1A / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 1.1Apr 24, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
A: 30S ribosomal protein S3Ae
B: 30S ribosomal protein S2
C: Zn-ribbon RNA-binding protein involved in translation
D: 30S ribosomal protein S4
E: 30S ribosomal protein S4e
F: 30S ribosomal protein S5
G: 30S ribosomal protein S6e
I: 30S ribosomal protein S8
J: 30S ribosomal protein S8e
M: 30S ribosomal protein S11
N: 30S ribosomal protein S12
Q: 30S ribosomal protein S15
R: 30S ribosomal protein S17
V: 30S ribosomal protein S24e
W: 30S ribosomal protein S27e
0: 30S ribosomal protein aL41
5: mRNA
6: Translation initiation factor 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)620,42549
Polymers619,49119
Non-polymers93530
Water46826
1


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

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Components

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RNA chain , 2 types, 2 molecules 25

#1: RNA chain 16S ribosomal RNA /


Mass: 340430.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)
#18: RNA chain mRNA / Messenger RNA


Mass: 6448.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea)

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30S ribosomal protein ... , 15 types, 15 molecules ABDEFGIJMNQRVW0

#2: Protein 30S ribosomal protein S3Ae / Ribosome / Ribosomal protein S1e


Mass: 22888.068 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: Q9V2K7
#3: Protein 30S ribosomal protein S2 /


Mass: 23026.865 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: Q9V191
#5: Protein 30S ribosomal protein S4 /


Mass: 21381.910 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: P61992
#6: Protein 30S ribosomal protein S4e / Ribosome


Mass: 28246.119 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: Q9V1U8
#7: Protein 30S ribosomal protein S5 /


Mass: 26523.904 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: Q9V1V5
#8: Protein 30S ribosomal protein S6e / Ribosome


Mass: 14029.461 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: Q9UYS3
#9: Protein 30S ribosomal protein S8 /


Mass: 14772.246 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: Q9V1V0
#10: Protein 30S ribosomal protein S8e / Ribosome


Mass: 14293.733 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: Q9UZL4
#11: Protein 30S ribosomal protein S11 /


Mass: 14772.950 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: P62010
#12: Protein 30S ribosomal protein S12 /


Mass: 16477.621 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: P61994
#13: Protein 30S ribosomal protein S15 /


Mass: 18697.143 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: Q9V2K9
#14: Protein 30S ribosomal protein S17 /


Mass: 13364.604 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: Q9V1U5
#15: Protein 30S ribosomal protein S24e / Ribosome


Mass: 11798.637 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: Q9UY20
#16: Protein 30S ribosomal protein S27e / Ribosome


Mass: 7186.609 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: Q9UXZ3
#17: Protein/peptide 30S ribosomal protein aL41 /


Mass: 4910.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U232*PLUS

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Protein , 2 types, 2 molecules C6

#4: Protein Zn-ribbon RNA-binding protein involved in translation


Mass: 7163.395 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: G8ZFK7
#19: 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, 56 molecules

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


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#21: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#22: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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

Component
IDNameTypeEntity IDParent-IDSource
1Archaeal translation initiation complex devoid of aIF1 - IC2 bodyRIBOSOME#1-#190MULTIPLE SOURCES
2ribosomeCOMPLEX#1-#171NATURAL
3mRNAMessenger RNACOMPLEX#181RECOMBINANT
4Translation initiation factor 1ACOMPLEX#191RECOMBINANT
Molecular weightValue: 1.05 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pyrococcus abyssi GE5 (archaea)272844
23Pyrococcus abyssi GE5 (archaea)272844
34Pyrococcus abyssi GE5 (archaea)272844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13synthetic construct (others)32630
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 FIELDBright-field microscopy
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01244573
ELECTRON MICROSCOPYf_angle_d0.98865458
ELECTRON MICROSCOPYf_dihedral_angle_d11.77724428
ELECTRON MICROSCOPYf_chiral_restr0.0568045
ELECTRON MICROSCOPYf_plane_restr0.0074309

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