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- PDB-4ue4: Structural basis for targeting and elongation arrest of Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 4ue4
TitleStructural basis for targeting and elongation arrest of Bacillus signal recognition particle
Components
  • 6S RNA
  • FTSQ SIGNAL SEQUENCE
  • SIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsTRANSLATION / SIGNAL RECOGNITION PARTICLE (SRP) / STALLED-RIBOSOME / TRANSLOCATION / MIFM STALLING
Function / homology
Function and homology information


FtsQBL complex / divisome complex / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division ...FtsQBL complex / divisome complex / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cell division / GTPase activity / GTP binding / ATP hydrolysis activity / identical protein binding / plasma membrane
Similarity search - Function
Cell division protein FtsQ, C-terminal / Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily ...Cell division protein FtsQ, C-terminal / Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Signal recognition particle protein / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / POTRA domain / POTRA domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Cell division protein FtsQ / Signal recognition particle protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsBeckert, B. / Kedrov, A. / Sohmen, D. / Kempf, G. / Wild, K. / Sinning, I. / Stahlberg, H. / Wilson, D.N. / Beckmann, R.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions.
Authors: Bertrand Beckert / Alexej Kedrov / Daniel Sohmen / Georg Kempf / Klemens Wild / Irmgard Sinning / Henning Stahlberg / Daniel N Wilson / Roland Beckmann /
Abstract: The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ...The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ribosomes are slowed down by the Alu domain of SRP to allow efficient targeting. In prokaryotes, however, little is known about the structure and function of Alu domain-containing SRPs. Here, we report a complete molecular model of SRP from the Gram-positive bacterium Bacillus subtilis, based on cryo-EM. The SRP comprises two subunits, 6S RNA and SRP54 or Ffh, and it facilitates elongation slowdown similarly to its eukaryotic counterpart. However, protein contacts with the small ribosomal subunit observed for the mammalian Alu domain are substituted in bacteria by RNA-RNA interactions of 6S RNA with the α-sarcin-ricin loop and helices H43 and H44 of 23S rRNA. Our findings provide a structural basis for cotranslational targeting and RNA-driven elongation arrest in prokaryotes.
History
DepositionDec 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_image_scans
Revision 1.4Oct 3, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: 6S RNA
B: FTSQ SIGNAL SEQUENCE
C: SIGNAL RECOGNITION PARTICLE PROTEIN


Theoretical massNumber of molelcules
Total (without water)100,0373
Polymers100,0373
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: RNA chain 6S RNA


Mass: 85909.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
References: GenBank: 40130
#2: Protein/peptide FTSQ SIGNAL SEQUENCE


Mass: 2466.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
References: UniProt: P06136*PLUS
#3: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / / FIFTY-FOUR HOMOLOG / FFH


Mass: 11660.719 Da / Num. of mol.: 1 / Fragment: M DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P37105

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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: BACILLUS SUBTILIS MIFM STALLED RIBOSOME IN COMPLEX WITH SIGNAL RECOGNITION PARTICLE (SRP)
Type: RIBOSOME
Buffer solutionName: HEPERS 20 MM, KOAC 150 MM, MG(OAC)2 10MM, NIKKOL 0.005%, DTT 1MM, 2% GLYCEROL
pH: 7.6
Details: HEPERS 20 MM, KOAC 150 MM, MG(OAC)2 10MM, NIKKOL 0.005%, DTT 1MM, 2% GLYCEROL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 10, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 7 Å / Num. of particles: 75900 / Actual pixel size: 0.953 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2843. (DEPOSITION ID: 12993).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Details: METHOD--RIGID BODY
RefinementHighest resolution: 7 Å
Refinement stepCycle: LAST / Highest resolution: 7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 5685 0 0 6181

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