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- PDB-5lmp: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiatio... -

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Entry
Database: PDB / ID: 5lmp
TitleStructure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C)
Components
  • (30S ribosomal protein ...) x 20
  • (Translation initiation factor IF- ...) x 2
  • 16S rRNA
  • mRNAMessenger RNA
KeywordsRIBOSOME / translation / initiation factors / 30S / IF1 / IF3 / PIC / Thermus thermophilus
Function / homology
Function and homology information


translation initiation factor activity / small ribosomal subunit / ribosome binding / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding ...translation initiation factor activity / small ribosomal subunit / ribosome binding / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Translation initiation factor IF-3, N-terminal domain / Ribosomal protein S19, superfamily / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S10 domain ...Translation initiation factor IF-3, N-terminal domain / Ribosomal protein S19, superfamily / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / 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 S14, type Z / Ribosomal protein S7 domain superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Translation initiation factor 3, C-terminal / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S3, conserved site / Ribosomal protein S11 / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 1A / IF-1 / 30S ribosomal protein Thx / Ribosomal protein S20 / Ribosomal protein S19 / Ribosomal protein S18 / Ribosomal protein S17 / Ribosomal protein S16 / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S13/S18 / Ribosomal protein S12/S23 / Ribosomal protein S10p/S20e / Ribosomal protein S18 superfamily / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S7p/S5e / Ribosomal protein S6 / Ribosomal protein S5, C-terminal domain / Ribosomal protein S5, N-terminal domain / S4 domain / Ribosomal protein S4/S9 N-terminal domain / KH domain / Ribosomal protein S3, C-terminal domain / Ribosomal protein S2 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Translation initiation factor 3, N-terminal / Ribosomal protein S19 conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S16 / 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 S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S6 / Ribosomal protein S13 / Ribosomal protein S15 / Ribosomal protein S8 / Ribosomal protein S14, conserved site / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S14 / Translation initiation factor 3 / Ribosomal protein S3, C-terminal / Ribosomal protein S18 / Ribosomal protein S10 / Ribosomal protein S15, bacterial-type / Ribosomal protein S5, C-terminal / Ribosomal protein S12, bacterial-type / Nucleic acid-binding, OB-fold / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / Ribosomal protein S13-like, H2TH
Translation initiation factor IF-1 / 30S ribosomal protein S4 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S17 / 30S ribosomal protein S8 / 30S ribosomal protein S7 / 30S ribosomal protein S2 / 30S ribosomal protein S3 / 30S ribosomal protein S9 / 30S ribosomal protein Thx ...Translation initiation factor IF-1 / 30S ribosomal protein S4 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S17 / 30S ribosomal protein S8 / 30S ribosomal protein S7 / 30S ribosomal protein S2 / 30S ribosomal protein S3 / 30S ribosomal protein S9 / 30S ribosomal protein Thx / 30S ribosomal protein S5 / 30S ribosomal protein S15 / 30S ribosomal protein S16 / Translation initiation factor IF-3 / 30S ribosomal protein S6 / 30S ribosomal protein S18 / gb:55771382: / 30S ribosomal protein S8 / 30S ribosomal protein S13 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S17 / 30S ribosomal protein S19 / 30S ribosomal protein S10 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S11
Biological speciesThermus thermophilus (bacteria)
Thermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.35 Å
AuthorsHussain, T. / Llacer, J.L. / Wimberly, B.T. / Ramakrishnan, V.
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 Report
SummaryFull reportAbout validation report
History
DepositionAug 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Derived calculations
Category: em_image_scans / em_software ...em_image_scans / em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name / _em_software.version
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c

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Structure visualization

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Assembly

Deposited unit
A: 16S rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
V: 30S ribosomal protein Thx
W: Translation initiation factor IF-1
X: Translation initiation factor IF-3
Y: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)826,828134
Polymers824,07224
Non-polymers2,756110
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area121370 Å2
ΔGint-1756 kcal/mol
Surface area274890 Å2
MethodPISA

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Components

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RNA chain , 2 types, 2 molecules AY

#1: RNA chain 16S rRNA


Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#24: RNA chain mRNA / Messenger RNA


Mass: 12525.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV

#2: Protein 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S ribosomal protein S9 /


Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12 /


Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17 /


Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19 /


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

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Translation initiation factor IF- ... , 2 types, 2 molecules WX

#22: Protein Translation initiation factor IF-1


Mass: 8247.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infA, TTHA1669 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHR1
#23: Protein Translation initiation factor IF-3


Mass: 19904.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infC, TTHA0551 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SKU2

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Non-polymers , 2 types, 110 molecules

#25: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Mg
#26: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 30S-IF1-IF3-mRNA pre-initiation complex (state-1C) / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
Source: MULTIPLE SOURCES
Molecular weightValue: 0.8261 MDa / Experimental value: NO
Buffer solutionpH: 7.5
Buffer component

Buffer-ID: 1

IDConc.Name
15 mMHepes-K
210 mMMagnessium acetate
350 mMPotassium chloride
410 mMAmmonium chloride
56 mMBeta mercaptoethanol
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 30 e/Å2 / Film or detector model: OTHER / Num. of grids imaged: 5 / Num. of real 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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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
2EMANparticle selection
3EPUimage acquisition
5CTFFIND3CTF correction
8UCSF Chimera1.1model fitting
9Coot0.8model fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15REFMAC5.8model refinement
Image processingDetails: FEI Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 666610
3D reconstructionResolution: 5.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18830 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: FSC

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