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- PDB-4ue5: Structural basis for targeting and elongation arrest of Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 4ue5
TitleStructural basis for targeting and elongation arrest of Bacillus signal recognition particle
Components
  • (SIGNAL RECOGNITION PARTICLE ...) x 3
  • 7S RNA
  • SIGNAL SEQUENCE
  • SRP14
  • SRP9
KeywordsTRANSLATION / STALLED RIBOSOME
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / absorption of visible light / negative regulation of translational elongation / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane ...SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle binding / absorption of visible light / negative regulation of translational elongation / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / 11-cis retinal binding / G protein-coupled photoreceptor activity / protein targeting to ER / cellular response to light stimulus / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / photoreceptor outer segment membrane / phototransduction / photoreceptor outer segment / neutrophil chemotaxis / visual perception / photoreceptor disc membrane / GDP binding / nuclear speck / G protein-coupled receptor signaling pathway / GTPase activity / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily ...Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / SRP/SRP receptor, N-terminal / Opsin / Signal recognition particle, SRP54 subunit / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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) / Signal recognition particle 19 kDa protein / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein / Rhodopsin / Signal recognition particle subunit SRP54 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesCANIS LUPUS FAMILIARIS (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 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 1.4Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_unobs_or_zero_occ_atoms ...database_PDB_caveat / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Revision 1.5Oct 3, 2018Group: Data collection / Derived calculations
Category: em_software / ndb_struct_na_base_pair ...em_software / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _em_software.image_processing_id
Revision 1.6Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.7May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2844
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  • Superimposition on EM map
  • EMDB-2844
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 7S RNA
B: SRP14
C: SIGNAL RECOGNITION PARTICLE SUBUNIT SRP68
D: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
E: SRP9
F: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
S: SIGNAL SEQUENCE


Theoretical massNumber of molelcules
Total (without water)199,9157
Polymers199,9157
Non-polymers00
Water00
1


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

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Components

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Protein , 2 types, 2 molecules BE

#2: Protein SRP14


Mass: 8604.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / References: UniProt: P16255*PLUS
#5: Protein SRP9


Mass: 8694.115 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-75 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / References: UniProt: P21262

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SIGNAL RECOGNITION PARTICLE ... , 3 types, 3 molecules CDF

#3: Protein SIGNAL RECOGNITION PARTICLE SUBUNIT SRP68 / SRP68 / SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN


Mass: 23220.695 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 55-249 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / References: UniProt: Q00004
#4: Protein SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN / SRP54


Mass: 48056.457 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-433 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / References: UniProt: P61010
#6: Protein SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN / SRP9


Mass: 12430.492 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-120 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / References: UniProt: J9PAS6

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RNA chain / Protein/peptide , 2 types, 2 molecules AS

#1: RNA chain 7S RNA


Mass: 96787.250 Da / Num. of mol.: 1 / Fragment: SRP RNA / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog)
#7: Protein/peptide SIGNAL SEQUENCE


Mass: 2121.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CANIS LUPUS FAMILIARIS (dog) / References: UniProt: P32308*PLUS

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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: MAMMALIAN SIGNAL RECOGNITION PARTICLE BOUND TO RIBOSOME NASCENT CHAIN COMPLEX
Type: RIBOSOME
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: Mar 3, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / 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: 9 Å / Num. of particles: 19096 / Actual pixel size: 1.24 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2844. (DEPOSITION ID: 12994).
Symmetry type: POINT
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 6403 0 0 9948

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