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- EMDB-56034: 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A) -

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Basic information

Entry
Database: EMDB / ID: EMD-56034
Title30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)
Map data30SICI
Sample
  • Complex: 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)
    • Protein or peptide: x 22 types
    • RNA: x 3 types
  • Ligand: x 2 types
KeywordsTranslation Initiation / time-resolved cryo-electron microscopy / GTP hydrolysis / initiation factor 1 / initiation factor 2 / RIBOSOME
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 / ribosome binding / 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-1 / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / : / Elongation factor G domain 2 ...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-1 / 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 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / 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 / Ribosomal protein S1-like RNA-binding domain / 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 / S1 domain / 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
Similarity search - Domain/homology
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 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 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGuerra GS / Demo G
Funding support Czech Republic, 1 items
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 GS / Zafar H / Ge X / Basu RS / Huang C / Hassan AH / Valdez NA / Brabencova S / Slamova L / Mandava CS / Gamper H / Hou Y / Gagnon MG / Sanyal S / Demo G
History
DepositionDec 10, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56034.png

Downloads & links

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Map

FileDownload / File: emd_56034.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation30SICI
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-4.89464 - 18.570408
Average (Standard dev.)0.0046241563 (±0.7869136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 400.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 30SICI

Fileemd_56034_half_map_1.map
Annotation30SICI
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 30SICI

Fileemd_56034_half_map_2.map
Annotation30SICI
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)

EntireName: 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)
Components
  • Complex: 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)
    • Protein or peptide: Small ribosomal subunit protein uS2
    • Protein or peptide: Small ribosomal subunit protein uS3
    • Protein or peptide: Small ribosomal subunit protein uS4
    • Protein or peptide: Small ribosomal subunit protein uS5
    • Protein or peptide: Small ribosomal subunit protein bS6, fully modified isoform
    • Protein or peptide: Small ribosomal subunit protein uS7
    • Protein or peptide: Small ribosomal subunit protein uS8
    • Protein or peptide: Small ribosomal subunit protein uS9
    • Protein or peptide: Small ribosomal subunit protein uS10
    • Protein or peptide: Small ribosomal subunit protein uS11
    • Protein or peptide: Small ribosomal subunit protein uS12
    • Protein or peptide: Small ribosomal subunit protein uS13
    • Protein or peptide: Small ribosomal subunit protein uS14
    • Protein or peptide: Small ribosomal subunit protein uS15
    • Protein or peptide: Small ribosomal subunit protein bS16
    • Protein or peptide: Small ribosomal subunit protein uS17
    • Protein or peptide: Small ribosomal subunit protein bS18
    • Protein or peptide: Small ribosomal subunit protein uS19
    • Protein or peptide: Small ribosomal subunit protein bS20
    • Protein or peptide: Small ribosomal subunit protein bS21
    • RNA: 16S Ribosomal RNA
    • RNA: mRNA
    • RNA: tRNAfMet
    • Protein or peptide: Translation initiation factor IF-1
    • Protein or peptide: Translation initiation factor IF-2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)

SupramoleculeName: 30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.0 MDa

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Macromolecule #1: Small ribosomal subunit protein uS2

MacromoleculeName: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.78167 KDa
SequenceString: MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH ...String:
MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH EHIAIKEANN LGIPVFAIVD TNSDPDGVDF VIPGNDDAIR AVTLYLGAVA ATVREGRSQD LASQAEESFV EA E

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #2: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.031316 KDa
SequenceString: MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY ...String:
MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY REGRVPLHTL RADIDYNTSE AHTTYGVIGV KVWIFKGEIL GGMAAVEQPE KPAAQPKKQQ RKGRK

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #3: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.514199 KDa
SequenceString: MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP ...String:
MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP TWLEVDAGKM EGTFKRKPER SDLSADINEH LIVELYSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #4: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.629398 KDa
SequenceString:
MAHIEKQAGE LQEKLIAVNR VSKTVKGGRI FSFTALTVVG DGNGRVGFGY GKAREVPAAI QKAMEKARRN MINVALNNGT LQHPVKGVH TGSRVFMQPA SEGTGIIAGG AMRAVLEVAG VHNVLAKAYG STNPINVVRA TIDGLENMNS PEMVAAKRGK S VEEILGK

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #5: Small ribosomal subunit protein bS6, fully modified isoform

MacromoleculeName: Small ribosomal subunit protein bS6, fully modified isoform
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.727512 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA SPMVKAKDER RERRDDFANE TADDAEAGDS EEEEEE

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #6: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.055156 KDa
SequenceString:
MPRRRVIGQR KILPDPKFGS ELLAKFVNIL MVDGKKSTAE SIVYSALETL AQRSGKSELE AFEVALENVR PTVEVKSRRV GGSTYQVPV EVRPVRRNAL AMRWIVEAAR KRGDKSMALR LANELSDAAE NKGTAVKKRE DVHRMAEANK AFAHYRWLSL R SFSHQAGA SSKQPALGYL N

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #7: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.146557 KDa
SequenceString:
MSMQDPIADM LTRIRNGQAA NKAAVTMPSS KLKVAIANVL KEEGFIEDFK VEGDTKPELE LTLKYFQGKA VVESIQRVSR PGLRIYKRK DELPKVMAGL GIAVVSTSKG VMTDRAARQA GLGGEIICYV A

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #8: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.88627 KDa
SequenceString:
MAENQYYGTG RRKSSAARVF IKPGNGKIVI NQRSLEQYFG RETARMVVRQ PLELVDMVEK LDLYITVKGG GISGQAGAIR HGITRALME YDESLRSELR KAGFVTRDAR QVERKKVGLR KARRRPQFSK R

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #9: Small ribosomal subunit protein uS10

MacromoleculeName: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.755597 KDa
SequenceString:
MQNQRIRIRL KAFDHRLIDQ ATAEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH LRLVDIVEPT EKTVDALMR LDLAAGVDVQ ISLG

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #10: Small ribosomal subunit protein uS11

MacromoleculeName: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.870975 KDa
SequenceString:
MAKAPIRARK RVRKQVSDGV AHIHASFNNT IVTITDRQGN ALGWATAGGS GFRGSRKSTP FAAQVAAERC ADAVKEYGIK NLEVMVKGP GPGRESTIRA LNAAGFRITN ITDVTPIPHN GCRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #11: Small ribosomal subunit protein uS12

MacromoleculeName: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.768157 KDa
SequenceString:
MATVNQLVRK PRARKVAKSN VPALEACPQK RGVCTRVYTT TPKKPNSALR KVCRVRLTNG FEVTSYIGGE GHNLQEHSVI LIRGGRVKD LPGVRYHTVR GALDCSGVKD RKQARSKYGV KRPKA

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #12: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.128467 KDa
SequenceString:
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKPIKK

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #13: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.60656 KDa
SequenceString:
MAKQSMKARE VKRVALADKY FAKRAELKAI ISDVNASDED RWNAVLKLQT LPRDSSPSRQ RNRCRQTGRP HGFLRKFGLS RIKVREAAM RGEIPGLKKA SW

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #14: Small ribosomal subunit protein uS15

MacromoleculeName: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.290816 KDa
SequenceString:
MSLSTEATAK IVSEFGRDAN DTGSTEVQVA LLTAQINHLQ GHFAEHKKDH HSRRGLLRMV SQRRKLLDYL KRKDVARYTQ LIERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #15: Small ribosomal subunit protein bS16

MacromoleculeName: Small ribosomal subunit protein bS16 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.207572 KDa
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #16: Small ribosomal subunit protein uS17

MacromoleculeName: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.724491 KDa
SequenceString:
MTDKIRTLQG RVVSDKMEKS IVVAIERFVK HPIYGKFIKR TTKLHVHDEN NECGIGDVVE IRECRPLSKT KSWTLVRVVE KAVL

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #17: Small ribosomal subunit protein bS18

MacromoleculeName: Small ribosomal subunit protein bS18 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.005472 KDa
SequenceString:
MARYFRRRKF CRFTAEGVQE IDYKDIATLK NYITESGKIV PSRITGTRAK YQRQLARAIK RARYLSLLPY TDRHQ

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #18: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.455355 KDa
SequenceString:
MPRSLKKGPF IDLHLLKKVE KAVESGDKKP LRTWSRRSTI FPNMIGLTIA VHNGRQHVPV FVTDEMVGHK LGEFAPTRTY RGHAADKKA KKK

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #19: Small ribosomal subunit protein bS20

MacromoleculeName: Small ribosomal subunit protein bS20 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.708464 KDa
SequenceString:
MANIKSAKKR AIQSEKARKH NASRRSMMRT FIKKVYAAIE AGDKAAAQKA FNEMQPIVDR QAAKGLIHKN KAARHKANLT AQINKLA

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #20: Small ribosomal subunit protein bS21

MacromoleculeName: Small ribosomal subunit protein bS21 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.524039 KDa
SequenceString:
MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKKL ARENARRTRL Y

UniProtKB: Small ribosomal subunit protein bS21

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Macromolecule #24: Translation initiation factor IF-1

MacromoleculeName: Translation initiation factor IF-1 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.091471 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MHHHHHHAKE DNIEMQGTVL ETLPNTMFRV ELENGHVVTA HISGKMRKNY IRILTGDKVT VELTPYDLSK GRIVFRSR

UniProtKB: Translation initiation factor IF-1

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Macromolecule #25: Translation initiation factor IF-2

MacromoleculeName: Translation initiation factor IF-2 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 98.327062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHTDV TIKTLAAERQ TSVERLVQQF ADAGIRKSAD DSVSAQEKQT LIDHLNQKNS GPDKLTLQRK TRSTLNIPGT GGKSKSVQI EVRKKRTFVK RDPQEAERLA AEEQAQREAE EQARREAEES AKREAQQKAE REAAEQAKRE AAEQAKREAA E KDKVSNQQ ...String:
MHHHHHHTDV TIKTLAAERQ TSVERLVQQF ADAGIRKSAD DSVSAQEKQT LIDHLNQKNS GPDKLTLQRK TRSTLNIPGT GGKSKSVQI EVRKKRTFVK RDPQEAERLA AEEQAQREAE EQARREAEES AKREAQQKAE REAAEQAKRE AAEQAKREAA E KDKVSNQQ DDMTKNAQAE KARREQEAAE LKRKAEEEAR RKLEEEARRV AEEARRMAEE NKWTDNAEPT EDSSDYHVTT SQ HARQAED ESDREVEGGR GRGRNAKAAR PKKGNKHAES KADREEARAA VRGGKGGKRK GSSLQQGFQK PAQAVNRDVV IGE TITVGE LANKMAVKGS QVIKAMMKLG AMATINQVID QETAQLVAEE MGHKVILRRE NELEEAVMSD RDTGAAAEPR APVV TIMGH VDHGKTSLLD YIRSTKVASG EAGGITQHIG AYHVETENGM ITFLDTPGHA AFTSMRARGA QATDIVVLVV AADDG VMPQ TIEAIQHAKA AQVPVVVAVN KIDKPEADPD RVKNELSQYG ILPEEWGGES QFVHVSAKAG TGIDELLDAI LLQAEV LEL KAVRKGMASG AVIESFLDKG RGPVATVLVR EGTLHKGDIV LCGFEYGRVR AMRNELGQEV LEAGPSIPVE ILGLSGV PA AGDEVTVVRD EKKAREVALY RQGKFREVKL ARQQKSKLEN MFANMTEGEV HEVNIVLKAD VQGSVEAISD SLLKLSTD E VKVKIIGSGV GGITETDATL AAASNAILVG FNVRADASAR KVIEAESLDL RYYSVIYNLI DEVKAAMSGM LSPELKQQI IGLAEVRDVF KSPKFGAIAG CMVTEGVVKR HNPIRVLRDN VVIYEGELES LRRFKDDVNE VRNGMECGIG VKNYNDVRTG DVIEVFEII EIQRTIA

UniProtKB: Translation initiation factor IF-2

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Macromolecule #21: 16S Ribosomal RNA

MacromoleculeName: 16S Ribosomal RNA / type: rna / ID: 21 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 499.031562 KDa
SequenceString: AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC ...String:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC UAAUACCGCA UAACGUCGCA AGACCAAAGA GGGGGACCUU CGGGCCUCUU GCCAUCGGAU GUGCCCAGAU GG GAUUAGC UAGUAGGUGG GGUAACGGCU CACCUAGGCG ACGAUCCCUA GCUGGUCUGA GAGGAUGACC AGCCACACUG GAA CUGAGA CACGGUCCAG ACUCCUACGG GAGGCAGCAG UGGGGAAUAU UGCACAAUGG GCGCAAGCCU GAUGCAGCCA UGCC GCGUG UAUGAAGAAG GCCUUCGGGU UGUAAAGUAC UUUCAGCGGG GAGGAAGGGA GUAAAGUUAA UACCUUUGCU CAUUG ACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAU UAC UGGGCGUAAA GCGCACGCAG GCGGUUUGUU AAGUCAGAUG UGAAAUCCCC GGGCUCAACC UGGGAACUGC AUCUGAU AC UGGCAAGCUU GAGUCUCGUA GAGGGGGGUA GAAUUCCAGG UGUAGCGGUG AAAUGCGUAG AGAUCUGGAG GAAUACCG G UGGCGAAGGC GGCCCCCUGG ACGAAGACUG ACGCUCAGGU GCGAAAGCGU GGGGAGCAAA CAGGAUUAGA UACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU U CGAUGCAA CGCGAAGAAC CUUACCUGGU CUUGACAUCC ACGGAAGUUU UCAGAGAUGA GAAUGUGCCU UCGGGAACCG UG AGACAGG UGCUGCAUGG CUGUCGUCAG CUCGUGUUGU GAAAUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCUUAU CCU UUGUUG CCAGCGGUCC GGCCGGGAAC UCAAAGGAGA CUGCCAGUGA UAAACUGGAG GAAGGUGGGG AUGACGUCAA GUCA UCAUG GCCCUUACGA CCAGGGCUAC ACACGUGCUA CAAUGGCGCA UACAAAGAGA AGCGACCUCG CGAGAGCAAG CGGAC CUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAG AAU GCCACGGUGA AUACGUUCCC GGGCCUUGUA CACACCGCCC GUCACACCAU GGGAGUGGGU UGCAAAAGAA GUAGGUA GC UUAACCUUCG GGAGGGCGCU UACCACUUUG UGAUUCAUGA CUGGGGUGAA GUCGUAACAA GGUAACCGUA GGGGAACC U GCGGUUGGAU CACCUCCUU

GENBANK: GENBANK: CP194060.1

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Macromolecule #22: mRNA

MacromoleculeName: mRNA / type: rna / ID: 22 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.05782 KDa
SequenceString:
GCAAAGGAGG UAAAAAUGGU UACACUCAAG AUUGCCAUCA UUGACUUAGC CGGACA

+
Macromolecule #23: tRNAfMet

MacromoleculeName: tRNAfMet / type: rna / ID: 23 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.802785 KDa
SequenceString:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGGUCG UCGGUUCAAA UCCGGCCCCC GCAACCA

GENBANK: GENBANK: AP023205.1

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Macromolecule #26: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 26 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

+
Macromolecule #27: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 27 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H12ClNO3Tris hydrochloride
50.0 mMKClPotassium chloride
10.0 mMMg(OAC)2Magnesium acetate
4.0 mMC2H6OS2-Mercaptoethanol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 17477 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 / Details: Movie-mode at 20 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1889196
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wdd

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 22197
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: FREALIGN (ver. 9.11)

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Atomic model buiding 1

Initial modelPDB ID:

6wdd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9tkn:
30S pre-initiation complex with IF2 and IF1 bound (30S PIC-A)

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