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- EMDB-4073: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiatio... -

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Entry
Database: EMDB / ID: 4073
TitleStructure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A)
Map dataFor optimal visualization of IF3 N-terminal domain, gauss-filter de map by 1.1 and display it at 0.05 contour
Sample30S-IF1-IF3-mRNA pre-initiation complex (state-1A)
  • (nucleic-acidNucleic acid) x 2
  • (30S ribosomal protein ...) x 20
  • (Translation initiation factor IF- ...) x 2
  • (ligand) x 2
Function / homologyRibosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily ...Ribosomal protein S6 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S2 / Ribosomal protein S6 signature. / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S15 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S7, conserved site / 30S ribosomal protein Thx / Ribosomal protein S4 signature. / Ribosomal protein S5 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Ribosomal protein S7 signature. / KH domain / Ribosomal protein S10p/S20e / Translation initiation factor IF-3, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / Translation initiation factor 1A / IF-1 / Ribosomal protein S18 / Ribosomal protein S16 / Translation initiation factor IF-3, C-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S9, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S3, C-terminal / Ribosomal protein S15, bacterial-type / Translation initiation factor IF-1 / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Translation initiation factor 3 / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S14 / Ribosomal protein S5 / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / S1 domain IF1 type profile. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / Ribosomal protein S5, C-terminal
Function and homology information
SourceThermus thermophilus HB8 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.55 Å resolution
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.
Validation ReportPDB-ID: 5lmn

SummaryFull reportAbout validation report
DateDeposition: Aug 1, 2016 / Header (metadata) release: Aug 24, 2016 / Map release: Oct 5, 2016 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
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  • Surface view colored by height
  • Surface level: 0.09
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  • Surface view with fitted model
  • Atomic models: : PDB-5lmn
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4073.map.gz (map file in CCP4 format, 70305 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
1.34 Å/pix.
= 348.4 Å
260 pix
1.34 Å/pix.
= 348.4 Å
260 pix
1.34 Å/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
Contour Level:0.09 (by author), 0.09 (movie #1):
Minimum - Maximum-0.36352223 - 0.9275878
Average (Standard dev.)-0.000101041 (0.029434646)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions260260260
Origin000
Limit259259259
Spacing260260260
CellA=B=C: 348.4 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.3640.928-0.000

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Supplemental data

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Sample components

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Entire 30S-IF1-IF3-mRNA pre-initiation complex (state-1A)

EntireName: 30S-IF1-IF3-mRNA pre-initiation complex (state-1A) / Number of components: 27
MassTheoretical: 826.1 kDa

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Component #1: protein, 30S-IF1-IF3-mRNA pre-initiation complex (state-1A)

ProteinName: 30S-IF1-IF3-mRNA pre-initiation complex (state-1A) / Recombinant expression: No
MassTheoretical: 826.1 kDa

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Component #2: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUGUUGGAG AGUUUGAUCC UGGCUCAGGG UGAACGCUGG CGGCGUGCCU AAGACAUGCA AGUCGUGCGG GCCGCGGGGU UUUACUCCGU GGUCAGCGGC GGACGGGUGA GUAACGCGUG GGUGACCUAC CCGGAAGAGG GGGACAACCC GGGGAAACUC GGGCUAAUCC CCCAUGUGGA CCCGCCCCUU GGGGUGUGUC CAAAGGGCUU UGCCCGCUUC CGGAUGGGCC CGCGUCCCAU CAGCUAGUUG GUGGGGUAAU GGCCCACCAA GGCGACGACG GGUAGCCGGU CUGAGAGGAU GGCCGGCCAC AGGGGCACUG AGACACGGGC CCCACUCCUA CGGGAGGCAG CAGUUAGGAA UCUUCCGCAA UGGGCGCAAG CCUGACGGAG CGACGCCGCU UGGAGGAAGA AGCCCUUCGG GGUGUAAACU CCUGAACCCG GGACGAAACC CCCGACGAGG GGACUGACGG UACCGGGGUA AUAGCGCCGG CCAACUCCGU GCCAGCAGCC GCGGUAAUAC GGAGGGCGCG AGCGUUACCC GGAUUCACUG GGCGUAAAGG GCGUGUAGGC GGCCUGGGGC GUCCCAUGUG AAAGACCACG GCUCAACCGU GGGGGAGCGU GGGAUACGCU CAGGCUAGAC GGUGGGAGAG GGUGGUGGAA UUCCCGGAGU AGCGGUGAAA UGCGCAGAUA CCGGGAGGAA CGCCGAUGGC GAAGGCAGCC ACCUGGUCCA CCCGUGACGC UGAGGCGCGA AAGCGUGGGG AGCAAACCGG AUUAGAUACC CGGGUAGUCC ACGCCCUAAA CGAUGCGCGC UAGGUCUCUG GGUCUCCUGG GGGCCGAAGC UAACGCGUUA AGCGCGCCGC CUGGGGAGUA CGGCCGCAAG GCUGAAACUC AAAGGAAUUG ACGGGGGCCC GCACAAGCGG UGGAGCAUGU GGUUUAAUUC GAAGCAACGC GAAGAACCUU ACCAGGCCUU GACAUGCUAG GGAACCCGGG UGAAAGCCUG GGGUGCCCCG CGAGGGGAGC CCUAGCACAG GUGCUGCAUG GCCGUCGUCA GCUCGUGCCG UGAGGUGUUG GGUUAAGUCC CGCAACGAGC GCAACCCCCG CCGUUAGUUG CCAGCGGUUC GGCCGGGCAC UCUAACGGGA CUGCCCGCGA AAGCGGGAGG AAGGAGGGGA CGACGUCUGG UCAGCAUGGC CCUUACGGCC UGGGCGACAC ACGUGCUACA AUGCCCACUA CAAAGCGAUG CCACCCGGCA ACGGGGAGCU AAUCGCAAAA AGGUGGGCCC AGUUCGGAUU GGGGUCUGCA ACCCGACCCC AUGAAGCCGG AAUCGCUAGU AAUCGCGGAU CAGCCAUGCC GCGGUGAAUA CGUUCCCGGG CCUUGUACAC ACCGCCCGUC ACGCCAUGGG AGCGGGCUCU ACCCGAAGUC GCCGGGAGCC UACGGGCAGG CGCCGAGGGU AGGGCCCGUG ACUGGGGCGA AGUCGUAACA AGGUAGCUGU ACCGGAAGGU GCGGCUGGAU CACCUCCUUU CU
MassTheoretical: 493.958281 kDa
SourceSpecies: Thermus thermophilus HB8 (bacteria)

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 29.317703 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 26.751076 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 24.373447 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Details: Uniprot code Q5SHQ5 / Recombinant expression: No
MassTheoretical: 17.583416 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #7: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Details: Uniprot code Q5SLP8 / Recombinant expression: No
MassTheoretical: 11.988753 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Details: Uniprot code P17291 / Recombinant expression: No
MassTheoretical: 18.050973 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Details: Uniprot code Q5SHQ2 / Recombinant expression: No
MassTheoretical: 15.86857 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Details: Uniprot code P80374 / Recombinant expression: No
MassTheoretical: 14.410614 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Details: Uniprot code Q5SHN7 / Recombinant expression: No
MassTheoretical: 11.954968 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Details: Uniprot code P80376 / Recombinant expression: No
MassTheoretical: 13.737868 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Details: Uniprot code Q5SHN3 / Recombinant expression: No
MassTheoretical: 14.637384 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Details: P80377 / Recombinant expression: No
MassTheoretical: 14.338861 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #15: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Details: Q5SHQ1 / Recombinant expression: No
MassTheoretical: 7.158725 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Details: Q5SJ76 / Recombinant expression: No
MassTheoretical: 10.578407 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #17: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Details: Q5SJH3 / Recombinant expression: No
MassTheoretical: 10.409983 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Details: Q5SHP7 / Recombinant expression: No
MassTheoretical: 12.325655 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Details: Q5SLQ0 / Recombinant expression: No
MassTheoretical: 10.258299 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Details: Q5SHP2 / Recombinant expression: No
MassTheoretical: 10.605464 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Details: P80380 / Recombinant expression: No
MassTheoretical: 11.736143 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #22: protein, 30S ribosomal protein Thx

ProteinName: 30S ribosomal protein ThxRibosome / Details: Q5SIH3 / Recombinant expression: No
MassTheoretical: 3.35003 kDa
SourceSpecies: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #23: protein, Translation initiation factor IF-1

ProteinName: Translation initiation factor IF-1 / Details: Q5SHR1 / Recombinant expression: No
MassTheoretical: 8.247664 kDa
Source (engineered)Expression System: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #24: protein, Translation initiation factor IF-3

ProteinName: Translation initiation factor IF-3 / Details: Q5SKU2 / Recombinant expression: No
MassTheoretical: 19.904377 kDa
Source (engineered)Expression System: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579

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Component #25: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCUCUUUUAA CAAUUUAUCA GGCAAGGAGG UAAAAAUGUU CA
MassTheoretical: 13.466019 kDa

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Component #26: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 127 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #27: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.08 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000 X (nominal), 104478 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderModel: OTHER / Temperature: K ( 90 - 100 K)
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 4400
Details: Recorded in a FEI Falcon III direct electron detector. Images were collected in movie-mode at 32 frames per second

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 86892 / Details: FEI Falcon III
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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