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- PDB-9tko: 30S pre-initiation complex with IF2 bound (30S PIC-B) -

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Basic information

Entry
Database: PDB / ID: 9tko
Title30S pre-initiation complex with IF2 bound (30S PIC-B)
Components
  • (Small ribosomal subunit protein ...) x 20
  • 16S Ribosomal RNA
  • Translation initiation factor IF-2
  • mRNA
  • tRNAfMet
KeywordsRIBOSOME / Translation Initiation / time-resolved cryo-electron microscopy / GTP hydrolysis / initiation factor 1 / initiation factor 2
Function / homology
Function and homology information


guanosine tetraphosphate binding / ribosomal small subunit binding / transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / response to cold / regulation of mRNA stability ...guanosine tetraphosphate binding / ribosomal small subunit binding / transcription antitermination factor activity, RNA binding / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / response to cold / regulation of mRNA stability / translation initiation factor activity / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / regulation of DNA-templated transcription elongation / transcription antitermination / DNA endonuclease activity / molecular condensate scaffold activity / translational initiation / regulation of translation / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit assembly / ribosome biogenesis / protein folding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / hydrolase activity / ribosome / translation / structural constituent of ribosome / response to antibiotic / mRNA binding / GTPase activity / GTP binding / DNA-templated transcription / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 / Translation initiation factor IF- 2, domain 3 ...Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Elongation factor Tu domain 2 / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Small GTP-binding protein 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 S10 / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S2, conserved site / : / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-2 ...GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-2 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsGuerra, G.S. / Demo, G.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation26-20643S Czech Republic
CitationJournal: To Be Published
Title: Time-resolved visualization of IF1- and IF2-driven translation initiation in bacteria
Authors: Guerra, G.S. / Zafar, H. / Ge, X. / Basu, R.S. / Huang, C. / Hassan, A.H. / Valdez, N.A. / Brabencova, S. / Slamova, L. / Mandava, C.S. / Gamper, H. / Hou, Y. / Gagnon, M.G. / Sanyal, S. / Demo, G.
History
DepositionDec 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: Small ribosomal subunit protein uS2
AB: Small ribosomal subunit protein uS3
AC: Small ribosomal subunit protein uS4
AD: Small ribosomal subunit protein uS5
AE: Small ribosomal subunit protein bS6, fully modified isoform
AF: Small ribosomal subunit protein uS7
AG: Small ribosomal subunit protein uS8
AH: Small ribosomal subunit protein uS9
AI: Small ribosomal subunit protein uS10
AJ: Small ribosomal subunit protein uS11
AK: Small ribosomal subunit protein uS12
AL: Small ribosomal subunit protein uS13
AM: Small ribosomal subunit protein uS14
AN: Small ribosomal subunit protein uS15
AO: Small ribosomal subunit protein bS16
AP: Small ribosomal subunit protein uS17
AQ: Small ribosomal subunit protein bS18
AR: Small ribosomal subunit protein uS19
AT: Small ribosomal subunit protein bS20
AU: Small ribosomal subunit protein bS21
D1: 16S Ribosomal RNA
D4: mRNA
D5: tRNAfMet
F2: Translation initiation factor IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)930,45426
Polymers929,90624
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 20 types, 20 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARATAU

#1: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#2: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V3
#3: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#4: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W1
#5: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#6: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#7: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#8: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7X3
#9: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10 / Transcription termination/antitermination protein NusE


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R5
#10: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#11: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#12: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S9
#13: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG59
#14: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#15: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3
#16: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#17: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#18: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U3
#19: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#20: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P68679

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RNA chain , 3 types, 3 molecules D1D4D5

#21: RNA chain 16S Ribosomal RNA


Mass: 499031.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP194060.1
#22: RNA chain mRNA


Mass: 18057.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#23: RNA chain tRNAfMet


Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1848851804

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Protein , 1 types, 1 molecules F2

#24: Protein Translation initiation factor IF-2


Mass: 98327.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infB, gicD, ssyG, b3168, JW3137 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A705

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Non-polymers , 2 types, 2 molecules

#25: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#26: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: 30S pre-initiation complex with IF2 bound (30S PIC-B) / Type: RIBOSOME / Entity ID: #1-#24 / Source: NATURAL
Molecular weightValue: 1.0 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris hydrochlorideC4H12ClNO31
250 mMPotassium chlorideKCl1
310 mMMagnesium acetateMg(OAC)21
44 mM2-MercaptoethanolC2H6OS1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17477 / Details: Movie-mode at 20 frames per second

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Processing

EM software
IDNameVersionCategory
1cisTEM1.1.0particle selection
2PHENIX1.21.2_5419model refinement
5CTFFIND4CTF correction
10FREALIGN9.11initial Euler assignment
11FREALIGN9.11final Euler assignment
13FREALIGN9.113D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1889196
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28862 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6WDD

6wdd


Accession code: 6WDD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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