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- EMDB-4080: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-init... -

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Basic information

Entry
Database: EMDB / ID: EMD-4080
TitleStructure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, closed form (state-4)
Map dataFor optimal visualization of IF3, gauss-filter the map by 1.1 and display it at 0.05 contour
Sample
  • Complex: 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4)
    • RNA: x 3 types
    • Protein or peptide: x 21 types
  • Ligand: x 2 types
Keywordsribosome / translation / initiation factors / 30S / IF1 / IF3 / tRNAi / PIC / Thermus thermophilus
Function / homology
Function and homology information


translation initiation factor activity / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...translation initiation factor activity / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein ...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 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, 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 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 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 S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 ...Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Translation initiation factor IF-3 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsHussain T / Llacer JL
CitationJournal: Cell / Year: 2016
Title: Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.
Authors: Tanweer Hussain / Jose L Llácer / Brian T Wimberly / Jeffrey S Kieft / V Ramakrishnan /
Abstract: In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 ...In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition.
History
DepositionAug 1, 2016-
Header (metadata) releaseAug 17, 2016-
Map releaseOct 5, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lmu
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4080.png

Downloads & links

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Map

FileDownload / File: emd_4080.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFor optimal visualization of IF3, gauss-filter the map by 1.1 and display it at 0.05 contour
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 260 pix.
= 348.4 Å		1.34 Å/pix.
x 260 pix.
= 348.4 Å		1.34 Å/pix.
x 260 pix.
= 348.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.2714888 - 0.7036726
Average (Standard dev.)0.00013980691 (±0.028883386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 348.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z348.400348.400348.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.2710.7040.000

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Supplemental data

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Half map: #1

Fileemd_4080_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4080_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4)

EntireName: 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4)
Components
  • Complex: 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4)
    • RNA: 16S ribosomal RNA
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14 type Z
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein Thx
    • Protein or peptide: Translation initiation factor IF-3
    • RNA: mRNA
    • RNA: tRNAi
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4)

SupramoleculeName: 30S-IF1-IF3-mRNA-tRNA pre-initiation complex (state-4)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
Molecular weightTheoretical: 841.4 KDa

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Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 493.958281 KDa
SequenceString: UUUGUUGGAG AGUUUGAUCC UGGCUCAGGG UGAACGCUGG CGGCGUGCCU AAGACAUGCA AGUCGUGCGG GCCGCGGGGU UUUACUCCG UGGUCAGCGG CGGACGGGUG AGUAACGCGU GGGUGACCUA CCCGGAAGAG GGGGACAACC CGGGGAAACU C GGGCUAAU ...String:
UUUGUUGGAG AGUUUGAUCC UGGCUCAGGG UGAACGCUGG CGGCGUGCCU AAGACAUGCA AGUCGUGCGG GCCGCGGGGU UUUACUCCG UGGUCAGCGG CGGACGGGUG AGUAACGCGU GGGUGACCUA CCCGGAAGAG GGGGACAACC CGGGGAAACU C GGGCUAAU CCCCCAUGUG GACCCGCCCC UUGGGGUGUG UCCAAAGGGC UUUGCCCGCU UCCGGAUGGG CCCGCGUCCC AU CAGCUAG UUGGUGGGGU AAUGGCCCAC CAAGGCGACG ACGGGUAGCC GGUCUGAGAG GAUGGCCGGC CACAGGGGCA CUG AGACAC GGGCCCCACU CCUACGGGAG GCAGCAGUUA GGAAUCUUCC GCAAUGGGCG CAAGCCUGAC GGAGCGACGC CGCU UGGAG GAAGAAGCCC UUCGGGGUGU AAACUCCUGA ACCCGGGACG AAACCCCCGA CGAGGGGACU GACGGUACCG GGGUA AUAG CGCCGGCCAA CUCCGUGCCA GCAGCCGCGG UAAUACGGAG GGCGCGAGCG UUACCCGGAU UCACUGGGCG UAAAGG GCG UGUAGGCGGC CUGGGGCGUC CCAUGUGAAA GACCACGGCU CAACCGUGGG GGAGCGUGGG AUACGCUCAG GCUAGAC GG UGGGAGAGGG UGGUGGAAUU CCCGGAGUAG CGGUGAAAUG CGCAGAUACC GGGAGGAACG CCGAUGGCGA AGGCAGCC A CCUGGUCCAC CCGUGACGCU GAGGCGCGAA AGCGUGGGGA GCAAACCGGA UUAGAUACCC GGGUAGUCCA CGCCCUAAA CGAUGCGCGC UAGGUCUCUG GGUCUCCUGG GGGCCGAAGC UAACGCGUUA AGCGCGCCGC CUGGGGAGUA CGGCCGCAAG GCUGAAACU CAAAGGAAUU GACGGGGGCC CGCACAAGCG GUGGAGCAUG UGGUUUAAUU CGAAGCAACG CGAAGAACCU U ACCAGGCC UUGACAUGCU AGGGAACCCG GGUGAAAGCC UGGGGUGCCC CGCGAGGGGA GCCCUAGCAC AGGUGCUGCA UG GCCGUCG UCAGCUCGUG CCGUGAGGUG UUGGGUUAAG UCCCGCAACG AGCGCAACCC CCGCCGUUAG UUGCCAGCGG UUC GGCCGG GCACUCUAAC GGGACUGCCC GCGAAAGCGG GAGGAAGGAG GGGACGACGU CUGGUCAGCA UGGCCCUUAC GGCC UGGGC GACACACGUG CUACAAUGCC CACUACAAAG CGAUGCCACC CGGCAACGGG GAGCUAAUCG CAAAAAGGUG GGCCC AGUU CGGAUUGGGG UCUGCAACCC GACCCCAUGA AGCCGGAAUC GCUAGUAAUC GCGGAUCAGC CAUGCCGCGG UGAAUA CGU UCCCGGGCCU UGUACACACC GCCCGUCACG CCAUGGGAGC GGGCUCUACC CGAAGUCGCC GGGAGCCUAC GGGCAGG CG CCGAGGGUAG GGCCCGUGAC UGGGGCGAAG UCGUAACAAG GUAGCUGUAC CGGAAGGUGC GGCUGGAUCA CCUCCUUU C U

GENBANK: GENBANK: AP008226.1

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Macromolecule #23: mRNA

MacromoleculeName: mRNA / type: rna / ID: 23 / Number of copies: 1
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 13.466019 KDa
SequenceString:
GCUCUUUUAA CAAUUUAUCA GGCAAGGAGG UAAAAAUGUU CA

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Macromolecule #24: tRNAi

MacromoleculeName: tRNAi / type: rna / ID: 24 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.861938 KDa
SequenceString:
CGCGGGG(4SU)GG AGCAGCCUGG UAGCUCGUCG GG(OMC)UCAUAAC CCGAAG(G7M)UCG UCGG(5MU)(PSU)CAAA UCCGGCCCC CGCAACCA

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Macromolecule #2: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 29.317703 KDa
SequenceString: MPVEITVKEL LEAGVHFGHE RKRWNPKFAR YIYAERNGIH IIDLQKTMEE LERTFRFIED LAMRGGTILF VGTKKQAQDI VRMEAERAG MPYVNQRWLG GMLTNFKTIS QRVHRLEELE ALFASPEIEE RPKKEQVRLK HELERLQKYL SGFRLLKRLP D AIFVVDPT ...String:
MPVEITVKEL LEAGVHFGHE RKRWNPKFAR YIYAERNGIH IIDLQKTMEE LERTFRFIED LAMRGGTILF VGTKKQAQDI VRMEAERAG MPYVNQRWLG GMLTNFKTIS QRVHRLEELE ALFASPEIEE RPKKEQVRLK HELERLQKYL SGFRLLKRLP D AIFVVDPT KEAIAVREAR KLFIPVIALA DTDSDPDLVD YIIPGNDDAI RSIQLILSRA VDLIIQARGG VVEPSPSYAL VQ EAEATET PEGESEVEA

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 26.751076 KDa
SequenceString: MGNKIHPIGF RLGITRDWES RWYAGKKQYR HLLLEDQRIR GLLEKELYSA GLARVDIERA ADNVAVTVHV AKPGVVIGRG GERIRVLRE ELAKLTGKNV ALNVQEVQNP NLSAPLVAQR VAEQIERRFA VRRAIKQAVQ RVMESGAKGA KVIVSGRIGG A EQARTEWA ...String:
MGNKIHPIGF RLGITRDWES RWYAGKKQYR HLLLEDQRIR GLLEKELYSA GLARVDIERA ADNVAVTVHV AKPGVVIGRG GERIRVLRE ELAKLTGKNV ALNVQEVQNP NLSAPLVAQR VAEQIERRFA VRRAIKQAVQ RVMESGAKGA KVIVSGRIGG A EQARTEWA AQGRVPLHTL RANIDYGFAL ARTTYGVLGV KAYIFLGEVI GGQKPKARPE LPKAEERPRR RRPAVRVKKE E

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 24.373447 KDa
SequenceString: MGRYIGPVCR LCRREGVKLY LKGERCYSPK CAMERRPYPP GQHGQKRARR PSDYAVRLRE KQKLRRIYGI SERQFRNLFE EASKKKGVT GSVFLGLLES RLDNVVYRLG FAVSRRQARQ LVRHGHITVN GRRVDLPSYR VRPGDEIAVA EKSRNLELIR Q NLEAMKGR ...String:
MGRYIGPVCR LCRREGVKLY LKGERCYSPK CAMERRPYPP GQHGQKRARR PSDYAVRLRE KQKLRRIYGI SERQFRNLFE EASKKKGVT GSVFLGLLES RLDNVVYRLG FAVSRRQARQ LVRHGHITVN GRRVDLPSYR VRPGDEIAVA EKSRNLELIR Q NLEAMKGR KVGPWLSLDV EGMKGKFLRL PDREDLALPV NEQLVIEFYS R

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 17.583416 KDa
SequenceString:
MPETDFEEKM ILIRRTARMQ AGGRRFRFGA LVVVGDRQGR VGLGFGKAPE VPLAVQKAGY YARRNMVEVP LQNGTIPHEI EVEFGASKI VLKPAAPGTG VIAGAVPRAI LELAGVTDIL TKELGSRNPI NIAYATMEAL RQLRTKADVE RLRKGEAHAQ A QG

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #6: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 11.988753 KDa
SequenceString:
MRRYEVNIVL NPNLDQSQLA LEKEIIQRAL ENYGARVEKV EELGLRRLAY PIAKDPQGYF LWYQVEMPED RVNDLARELR IRDNVRRVM VVKSQEPFLA NA

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #7: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 18.050973 KDa
SequenceString:
MARRRRAEVR QLQPDLVYGD VLVTAFINKI MRDGKKNLAA RIFYDACKII QEKTGQEPLK VFKQAVENVK PRMEVRSRRV GGANYQVPM EVSPRRQQSL ALRWLVQAAN QRPERRAAVR IAHELMDAAE GKGGAVKKKE DVERMAEANR AYAHYRW

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #8: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 15.86857 KDa
SequenceString:
MLTDPIADML TRIRNATRVY KESTDVPASR FKEEILRILA REGFIKGYER VDVDGKPYLR VYLKYGPRRQ GPDPRPEQVI HHIRRISKP GRRVYVGVKE IPRVRRGLGI AILSTSKGVL TDREARKLGV GGELICEVW

UniProtKB: 30S ribosomal protein S8

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Macromolecule #9: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 14.410614 KDa
SequenceString:
MEQYYGTGRR KEAVARVFLR PGNGKVTVNG QDFNEYFQGL VRAVAALEPL RAVDALGHFD AYITVRGGGK SGQIDAIKLG IARALVQYN PDYRAKLKPL GFLTRDARVV ERKKYGKHKA RRAPQYSKR

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #10: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 11.954968 KDa
SequenceString:
MPKIRIKLRG FDHKTLDASA QKIVEAARRS GAQVSGPIPL PTRVRRFTVI RGPFKHKDSR EHFELRTHNR LVDIINPNRK TIEQLMTLD LPTGVEIEIK TVGGGR

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 13.737868 KDa
SequenceString:
MAKKPSKKKV KRQVASGRAY IHASYNNTIV TITDPDGNPI TWSSGGVIGY KGSRKGTPYA AQLAALDAAK KAMAYGMQSV DVIVRGTGA GREQAIRALQ ASGLQVKSIV DDTPVPHNGC RPKKKFRKAS

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 14.637384 KDa
SequenceString:
MPTINQLVRK GREKVRKKSK VPALKGAPFR RGVCTVVRTV TPKKPNSALR KVAKVRLTSG YEVTAYIPGE GHNLQEHSVV LIRGGRVKD LPGVRYHIVR GVYDAAGVKD RKKSRSKYGT KKPKEAAKTA AKK

UniProtKB: Small ribosomal subunit protein uS12

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Macromolecule #13: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 14.338861 KDa
SequenceString:
MARIAGVEIP RNKRVDVALT YIYGIGKARA KEALEKTGIN PATRVKDLTE AEVVRLREYV ENTWKLEGEL RAEVAANIKR LMDIGCYRG LRHRRGLPVR GQRTRTNART RKGPRKTVAG KKKAPRK

UniProtKB: Small ribosomal subunit protein uS13

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Macromolecule #14: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 7.158725 KDa
SequenceString:
MARKALIEKA KRTPKFKVRA YTRCVRCGRA RSVYRFFGLC RICLRELAHK GQLPGVRKAS W

UniProtKB: 30S ribosomal protein S14 type Z

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Macromolecule #15: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 10.578407 KDa
SequenceString:
MPITKEEKQK VIQEFARFPG DTGSTEVQVA LLTLRINRLS EHLKVHKKDH HSHRGLLMMV GQRRRLLRYL QREDPERYRA LIEKLGIRG

UniProtKB: Small ribosomal subunit protein uS15

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Macromolecule #16: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 10.409983 KDa
SequenceString:
MVKIRLARFG SKHNPHYRIV VTDARRKRDG KYIEKIGYYD PRKTTPDWLK VDVERARYWL SVGAQPTDTA RRLLRQAGVF RQEAREGA

UniProtKB: Small ribosomal subunit protein bS16

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Macromolecule #17: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 12.325655 KDa
SequenceString:
MPKKVLTGVV VSDKMQKTVT VLVERQFPHP LYGKVIKRSK KYLAHDPEEK YKLGDVVEII ESRPISKRKR FRVLRLVESG RMDLVEKYL IRRQNYESLS KRGGKA

UniProtKB: 30S ribosomal protein S17

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Macromolecule #18: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 10.258299 KDa
SequenceString:
MSTKNAKPKK EAQRRPSRKA KVKATLGEFD LRDYRNVEVL KRFLSETGKI LPRRRTGLSA KEQRILAKTI KRARILGLLP FTEKLVRK

UniProtKB: Small ribosomal subunit protein bS18

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Macromolecule #19: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 10.605464 KDa
SequenceString:
MPRSLKKGVF VDDHLLEKVL ELNAKGEKRL IKTWSRRSTI VPEMVGHTIA VYNGKQHVPV YITENMVGHK LGEFAPTRTY RGHGKEAKA TKKK

UniProtKB: Small ribosomal subunit protein uS19

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Macromolecule #20: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 11.736143 KDa
SequenceString:
MAQKKPKRNL SALKRHRQSL KRRLRNKAKK SAIKTLSKKA IQLAQEGKAE EALKIMRKAE SLIDKAAKGS TLHKNAAARR KSRLMRKVR QLLEAAGAPL IGGGLSA

UniProtKB: Small ribosomal subunit protein bS20

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Macromolecule #21: 30S ribosomal protein Thx

MacromoleculeName: 30S ribosomal protein Thx / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 3.35003 KDa
SequenceString:
MGKGDRRTRR GKIWRGTYGK YRPRKKK

UniProtKB: Small ribosomal subunit protein bTHX

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Macromolecule #22: Translation initiation factor IF-3

MacromoleculeName: Translation initiation factor IF-3 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 19.904377 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKEYLTNERI RAKQVRVVGP DGKQLGIMDT REALRLAQEM DLDLVLVGPN ADPPVARIMD YSKWRYEQQM AEKEARKKAK RTEVKSIKF RVKIDEHDYQ TKLGHIKRFL QEGHKVKVTI MFRGREVAHP ELGERILNRV TEDLKDLAVV EMKPEMLGRD M NMLLAPVK VSA

UniProtKB: Translation initiation factor IF-3

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Macromolecule #25: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 25 / Number of copies: 80 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #26: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 26 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.08 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
5.0 mMHepes-K
10.0 mMMagnessium acetate
50.0 mMPotassium chloride
10.0 mMAmmonium chloride
6.0 mMBeta mercaptoethanol
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90.0 K / Max: 100.0 K
Image recordingFilm or detector model: OTHER / Number grids imaged: 5 / Number real images: 4400 / Average exposure time: 1.1 sec. / Average electron dose: 30.0 e/Å2
Details: Recorded in a FEI Falcon III direct electron detector. Images were collected in movie-mode at 32 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsFEI Falcon III
Particle selectionNumber selected: 666610
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1hr0

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 26949
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final 3D classificationSoftware - Name: RELION (ver. 1.4)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: FSC
Output model

PDB-5lmu:
Structure of bacterial 30S-IF3-mRNA-tRNA translation pre-initiation complex, closed form (state-4)

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