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- EMDB-36619: Structure of the 30S-IF3 complex from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-36619
TitleStructure of the 30S-IF3 complex from Escherichia coli
Map dataMap of 30S-IF3 complex
Sample
  • Complex: Complex of the small ribosomal subunit (30S) and Translation initiation factor 3 (IF3) in Escherichia coli
    • Organelle or cellular component: Initiation factor 3
      • Protein or peptide: x 1 types
    • Organelle or cellular component: 30S subunit of ribosome
      • Protein or peptide: x 20 types
      • RNA: x 1 types
KeywordsRibosome / 30S / IF3 / Translation initiation / TRANSLATION
Function / homology
Function and homology information


mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity ...mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / transcription antitermination / maintenance of translational fidelity / DNA-templated transcription termination / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Ribosomal protein S21, conserved site ...Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / 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 S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / K Homology domain, type 2 / : / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S14 / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Type-2 KH domain profile. / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / S5 double stranded RNA-binding domain profile.
Similarity search - Domain/homology
Translation initiation factor IF-3 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 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 ...Translation initiation factor IF-3 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsUday AB / Mishra RK / Hussain T
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Proteins / Year: 2023
Title: Initiation factor 3 bound to the 30S ribosomal subunit in an initial step of translation.
Authors: Adwaith B Uday / Rishi Kumar Mishra / Tanweer Hussain /
Abstract: Bacterial ribosomes require three initiation factors IF1, IF2, and IF3 during the initial steps of translation. These IFs ensure correct base pairing of the initiator tRNA anticodon with the start ...Bacterial ribosomes require three initiation factors IF1, IF2, and IF3 during the initial steps of translation. These IFs ensure correct base pairing of the initiator tRNA anticodon with the start codon in the mRNA located at the P-site of the 30S ribosomal subunit. IF3 is one of the first IFs to bind to the 30S and plays a crucial role in the selection of the correct start codon and codon: anticodon base pairing. IF3 also prevents the premature association of the 50S subunit of ribosomes and aids in ribosome recycling. IF3 is reported to change binding sites and conformation to ensure translation initiation fidelity. A recent study suggested an initial binding of IF3 CTD away from the P-site and that IF1 and IF2 promote the movement of CTD to the P-site and concomitant movement of NTD. Hence, to visualize the position of IF3 in the absence of any other IFs, we determined cryo-EM structure of the 30S-IF3 complex. The map shows that IF3 is present in an extended conformation with CTD present at the P-site and NTD near the platform even in the absence of IF1 and IF2. Hence, IF3 CTD binds at the P-site and moves away during the accommodation of the initiator tRNA at the P-site in the later steps of translation initiation. Overall, we report the structure of 30S-IF3 which demystifies the starting binding site and conformation of IF3 on the 30S ribosomal subunit.
History
DepositionJun 20, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36619.png

Downloads & links

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Map

FileDownload / File: emd_36619.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of 30S-IF3 complex
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.00126
Minimum - Maximum-0.0020409403 - 0.02380403
Average (Standard dev.)0.00007340581 (±0.0014702815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36619_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_36619_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_36619_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the small ribosomal subunit (30S) and Translation init...

EntireName: Complex of the small ribosomal subunit (30S) and Translation initiation factor 3 (IF3) in Escherichia coli
Components
  • Complex: Complex of the small ribosomal subunit (30S) and Translation initiation factor 3 (IF3) in Escherichia coli
    • Organelle or cellular component: Initiation factor 3
      • Protein or peptide: Translation initiation factor IF-3
    • Organelle or cellular component: 30S subunit of ribosome
      • Protein or peptide: Small ribosomal subunit protein bS18
      • Protein or peptide: Small ribosomal subunit protein bS21
      • Protein or peptide: Small ribosomal subunit protein bS20
      • Protein or peptide: Small ribosomal subunit protein uS17
      • RNA: 16S ribosomal RNA
      • Protein or peptide: Small ribosomal subunit protein uS5
      • Protein or peptide: Small ribosomal subunit protein uS4
      • Protein or peptide: Small ribosomal subunit protein bS6, non-modified isoform
      • Protein or peptide: Small ribosomal subunit protein uS8
      • Protein or peptide: Small ribosomal subunit protein uS11
      • Protein or peptide: Small ribosomal subunit protein uS12
      • Protein or peptide: Small ribosomal subunit protein uS15
      • Protein or peptide: 30S ribosomal protein S16
      • Protein or peptide: Small ribosomal subunit protein uS3
      • Protein or peptide: Small ribosomal subunit protein uS7
      • Protein or peptide: Small ribosomal subunit protein uS9
      • Protein or peptide: Small ribosomal subunit protein uS10
      • Protein or peptide: Small ribosomal subunit protein uS13
      • Protein or peptide: Small ribosomal subunit protein uS14
      • Protein or peptide: Small ribosomal subunit protein uS19
      • Protein or peptide: Small ribosomal subunit protein uS2

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Supramolecule #1: Complex of the small ribosomal subunit (30S) and Translation init...

SupramoleculeName: Complex of the small ribosomal subunit (30S) and Translation initiation factor 3 (IF3) in Escherichia coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 850 KDa

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Supramolecule #2: Initiation factor 3

SupramoleculeName: Initiation factor 3 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: 30S subunit of ribosome

SupramoleculeName: 30S subunit of ribosome / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1-#3, #5-#22

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Macromolecule #1: Small ribosomal subunit protein bS18

MacromoleculeName: Small ribosomal subunit protein bS18 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.746147 KDa
SequenceString:
ARYFRRRKFC RFTAEGVQEI DYKDIATLKN YITESGKIVP SRITGTRAKY QRQLARAIKR ARYLSLLPYT DRH

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #2: Small ribosomal subunit protein bS21

MacromoleculeName: Small ribosomal subunit protein bS21 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.263326 KDa
SequenceString:
PVIKVRENEP FDVALRRFKR SCEKAGVLAE VRRREFYEKP TTERKRAKAS AVK

UniProtKB: Small ribosomal subunit protein bS21

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Macromolecule #3: Small ribosomal subunit protein bS20

MacromoleculeName: Small ribosomal subunit protein bS20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.577268 KDa
SequenceString:
ANIKSAKKRA IQSEKARKHN ASRRSMMRTF IKKVYAAIEA GDKAAAQKAF NEMQPIVDRQ AAKGLIHKNK AARHKANLTA QINKLA

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #4: Translation initiation factor IF-3

MacromoleculeName: Translation initiation factor IF-3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.600994 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKGGKRVQTA RPNRINGEIR AQEVRLTGLE GEQLGIVSLR EALEKAEEAG VDLVEISPNA EPPVCRIMDY GKFLYEKSKS SKEQKKKQK VIQVKEIKFR PGTDEGDYQV KLRSLIRFLE EGDKAKITLR FRGREMAHQQ IGMEVLNRVK DDLQELAVVE S FPTKIEGR QMIMVLAPKK KQ

UniProtKB: Translation initiation factor IF-3

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Macromolecule #5: Small ribosomal subunit protein uS17

MacromoleculeName: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.480138 KDa
SequenceString:
TDKIRTLQGR VVSDKMEKSI VVAIERFVKH PIYGKFIKRT TKLHVHDENN ECGIGDVVEI RECRPLSKTK SWTLVRVVEK AV

UniProtKB: Small ribosomal subunit protein uS17

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Macromolecule #7: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.641217 KDa
SequenceString:
AHIEKQAGEL QEKLIAVNRV SKTVKGGRIF SFTALTVVGD GNGRVGFGYG KAREVPAAIQ KAMEKARRNM INVALNNGTL QHPVKGVHT GSRVFMQPAS EGTGIIAGGA MRAVLEVAGV HNVLAKAYGS TNPINVVRAT IDGLENMNSP EMVAAKRGK

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.383002 KDa
SequenceString: ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT ...String:
ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT WLEVDAGKME GTFKRKPERS DLSADINEHL IVELYSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #9: Small ribosomal subunit protein bS6, non-modified isoform

MacromoleculeName: Small ribosomal subunit protein bS6, non-modified isoform
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.669371 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA S

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #10: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.015361 KDa
SequenceString:
SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #11: Small ribosomal subunit protein uS11

MacromoleculeName: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.739778 KDa
SequenceString:
AKAPIRARKR VRKQVSDGVA HIHASFNNTI VTITDRQGNA LGWATAGGSG FRGSRKSTPF AAQVAAERCA DAVKEYGIKN LEVMVKGPG PGRESTIRAL NAAGFRITNI TDVTPIPHNG CRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #12: Small ribosomal subunit protein uS12

MacromoleculeName: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.636961 KDa
SequenceString:
ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #13: Small ribosomal subunit protein uS15

MacromoleculeName: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.159621 KDa
SequenceString:
SLSTEATAKI VSEFGRDAND TGSTEVQVAL LTAQINHLQG HFAEHKKDHH SRRGLLRMVS QRRKLLDYLK RKDVARYTQL IERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #14: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 14 / 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 #15: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.078785 KDa
SequenceString: GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR ...String:
GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR EGRVPLHTLR ADIDYNTSEA HTTYGVIGVK VWIFKGEI

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #16: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.861523 KDa
SequenceString:
PRRRVIGQRK ILPDPKFGSE LLAKFVNILM VDGKKSTAES IVYSALETLA QRSGKSELEA FEVALENVRP TVEVKSRRVG GSTYQVPVE VRPVRRNALA MRWIVEAARK RGDKSMALRL ANELSDAAEN KGTAVKKRED VHRMAEANKA FA

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #17: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.755074 KDa
SequenceString:
AENQYYGTGR RKSSAARVFI KPGNGKIVIN QRSLEQYFGR ETARMVVRQP LELVDMVEKL DLYITVKGGG ISGQAGAIRH GITRALMEY DESLRSELRK AGFVTRDARQ VERKKVGLRK ARRRPQFSKR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #18: Small ribosomal subunit protein uS10

MacromoleculeName: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.698545 KDa
SequenceString:
MQNQRIRIRL KAFDHRLIDQ ATAEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH LRLVDIVEPT EKTVDALMR LDLAAGVDVQ ISL

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #19: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.625753 KDa
SequenceString:
ARIAGINIPD HKHAVIALTS IYGVGKTRSK AILAAAGIAE DVKISELSEG QIDTLRDEVA KFVVEGDLRR EISMSIKRLM DLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKP

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #20: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.475364 KDa
SequenceString:
AKQSMKAREV KRVALADKYF AKRAELKAII SDVNASDEDR WNAVLKLQTL PRDSSPSRQR NRCRQTGRPH GFLRKFGLSR IKVREAAMR GEIPGLKKAS W

UniProtKB: Small ribosomal subunit protein uS14

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Macromolecule #21: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.15474 KDa
SequenceString:
PRSLKKGPFI DLHLLKKVEK AVESGDKKPL RTWSRRSTIF PNMIGLTIAV HNGRQHVPVF VTDEMVGHKL GEFAPTRTYR

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #22: Small ribosomal subunit protein uS2

MacromoleculeName: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.015816 KDa
SequenceString: ATVSMRDMLK AGVHFGHQTR YWNPKMKPFI FGARNKVHII NLEKTVPMFN EALAELNKIA SRKGKILFVG TKRAASEAVK DAALSCDQF FVNHRWLGGM LTNWKTVRQS IKRLKDLETQ SQDGTFDKLT KKEALMRTRE LEKLENSLGG IKDMGGLPDA L FVIDADHE ...String:
ATVSMRDMLK AGVHFGHQTR YWNPKMKPFI FGARNKVHII NLEKTVPMFN EALAELNKIA SRKGKILFVG TKRAASEAVK DAALSCDQF FVNHRWLGGM LTNWKTVRQS IKRLKDLETQ SQDGTFDKLT KKEALMRTRE LEKLENSLGG IKDMGGLPDA L FVIDADHE HIAIKEANNL GIPVFAIVDT NSDPDGVDFV IPGNDDAIRA VTLYLGAVAA TVREGRS

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #6: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 499.077625 KDa
SequenceString: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUU CUUUGCUGAC GAGUGGCGGA CGGGUGAGUA AUGUCUGGGA AACUGCCUGA UGGAGGGGGA UAACUACUGG A AACGGUAG ...String:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUU CUUUGCUGAC GAGUGGCGGA CGGGUGAGUA AUGUCUGGGA AACUGCCUGA UGGAGGGGGA UAACUACUGG A AACGGUAG CUAAUACCGC AUAACGUCGC AAGACCAAAG AGGGGGACCU UCGGGCCUCU UGCCAUCGGA UGUGCCCAGA UG GGAUUAG CUAGUAGGUG GGGUAACGGC UCACCUAGGC GACGAUCCCU AGCUGGUCUG AGAGGAUGAC CAGCCACACU GGA ACUGAG ACACGGUCCA GACUCCUACG GGAGGCAGCA GUGGGGAAUA UUGCACAAUG GGCGCAAGCC UGAUGCAGCC AUGC CGCGU GUAUGAAGAA GGCCUUCGGG UUGUAAAGUA CUUUCAGCGG GGAGGAAGGG AGUAAAGUUA AUACCUUUGC UCAUU GACG UUACCCGCAG AAGAAGCACC GGCUAACUCC GUGCCAGCAG CCGCGGUAAU ACGGAGGGUG CAAGCGUUAA UCGGAA UUA CUGGGCGUAA AGCGCACGCA GGCGGUUUGU UAAGUCAGAU GUGAAAUCCC CGGGCUCAAC CUGGGAACUG CAUCUGA UA CUGGCAAGCU UGAGUCUCGU AGAGGGGGGU AGAAUUCCAG GUGUAGCGGU GAAAUGCGUA GAGAUCUGGA GGAAUACC G GUGGCGAAGG CGGCCCCCUG GACGAAGACU GACGCUCAGG UGCGAAAGCG UGGGGAGCAA ACAGGAUUAG AUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGA GUACGGCCGC AAGGUUAAAA CUCAAAUGAA AUGACGGGGG CCCGCACAAG CGGUGGAGCA UGUGGUUUAA U UCGAUGCA ACGCGAAGAA CCUUACCUGG UCUUGACAUC CACGGAAGUU UUCAGAGAUG AGAAUGUGCC UUCGGGAACC GU GAGACAG GUGCUGCAUG GCUGUCGUCA GCUCGUGUUG UGAAAUGUUG GGUUAAGUCC CGCAACGAGC GCAACCCUUA UCC UUUGUU GCCAGCGGUC CGGCCGGGAA CUCAAAGGAG ACUGCCAGUG AUAAACUGGA GGAAGGUGGG GAUGACGUCA AGUC AUCAU GGCCCUUACG ACCAGGGCUA CACACGUGCU ACAAUGGCGC AUACAAAGAG AAGCGACCUC GCGAGAGCAA GCGGA CCUC AUAAAGUGCG UCGUAGUCCG GAUUGGAGUC UGCAACUCGA CUCCAUGAAG UCGGAAUCGC UAGUAAUCGU GGAUCA GAA UGCCACGGUG AAUACGUUCC CGGGCCUUGU ACACACCGCC CGUCACACCA UGGGAGUGGG UUGCAAAAGA AGUAGGU AG CUUAACCUUC GGGAGGGCGC UUACCACUUU GUGAUUCAUG ACUGGGGUGA AGUCGUAACA AGGUAACCGU AGGGGAAC C UGCGGUUGGA UCACCUCCU

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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
5.0 mMC8H19KN2O5SHEPES-KOH
10.0 mMMg(CH3COO)2Magnesium acetate
50.0 mMKClPottasium chloride
10.0 mMNH4ClAmmonium chloride
6.0 mMC2H6OSBeta-mercaptoethanol2-Mercaptoethanol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 2 / Number real images: 4564 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6o7k

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145664
FSC plot (resolution estimation)

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