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- PDB-3zn8: Structural Basis of Signal Sequence Surveillance and Selection by... -

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Entry
Database: PDB / ID: 3zn8
TitleStructural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex
Components
  • (SIGNAL RECOGNITION PARTICLE ...) x 3
  • 4.5 S RNA
  • DIPEPTIDYL AMINOPEPTIDASE B
KeywordsPROTEIN TRANSPORT / HYDROLASE
Function / homology
Function and homology information


Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / fungal-type vacuole membrane / dipeptidyl-peptidase activity / stringent response ...Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / fungal-type vacuole membrane / dipeptidyl-peptidase activity / stringent response / protein targeting / aminopeptidase activity / cytoplasmic side of plasma membrane / protein processing / serine-type endopeptidase activity / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity / proteolysis / plasma membrane / cytosol
Similarity search - Function
Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / 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 ...Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / 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 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RNA / RNA (> 10) / Signal recognition particle protein / Signal recognition particle receptor FtsY / Dipeptidyl aminopeptidase B / Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
SULFOLOBUS SOLFATARICUS (archaea)
SACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
Authorsvon Loeffelholz, O. / Knoops, K. / Ariosa, A. / Zhang, X. / Karuppasamy, M. / Huard, K. / Schoehn, G. / Berger, I. / Shan, S.O. / Schaffitzel, C.
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex.
Authors: Ottilie von Loeffelholz / Kèvin Knoops / Aileen Ariosa / Xin Zhang / Manikandan Karuppasamy / Karine Huard / Guy Schoehn / Imre Berger / Shu-ou Shan / Christiane Schaffitzel /
Abstract: Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences ...Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences can be rejected from the targeting reaction even after they are bound to the SRP. Here we show that the early complex, formed by Escherichia coli SRP and its receptor FtsY with ribosomes translating the incorrect cargo EspP, is unstable and rearranges inefficiently into subsequent conformational states, such that FtsY dissociation is favored over successful targeting. The N-terminal extension of EspP is responsible for these defects in the early targeting complex. The cryo-electron microscopy structure of this 'false' early complex with EspP revealed an ordered M domain of SRP protein Ffh making two ribosomal contacts, and the NG domains of Ffh and FtsY forming a distorted, flexible heterodimer. Our results provide a structural basis for SRP-mediated signal-sequence selection during recruitment of the SRP receptor.
History
DepositionFeb 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3May 22, 2013Group: Database references
Revision 1.4Feb 26, 2014Group: Other / Refinement description
Revision 2.0Mar 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_distant_solvent_atoms / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.src_method
Revision 2.1Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
D: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
G: 4.5 S RNA
M: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
S: DIPEPTIDYL AMINOPEPTIDASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0836
Polymers109,0585
Non-polymers241
Water2,180121
1


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

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Components

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

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / / FIFTY-FOUR HOMOLOG


Mass: 32256.250 Da / Num. of mol.: 1 / Fragment: NG, RESIDUES 2-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21 (bacteria) / Strain (production host): STAR
References: UniProt: O07347, signal-recognition-particle GTPase
#2: Protein SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY / SRP RECEPTOR


Mass: 32182.012 Da / Num. of mol.: 1 / Fragment: NG, RESIDUES 201-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21 (bacteria) / Strain (production host): STAR
References: UniProt: P10121, signal-recognition-particle GTPase
#4: Protein SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN / SRP54 / FFH


Mass: 14591.145 Da / Num. of mol.: 1 / Fragment: M, RESIDUES 327-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI BL21 (bacteria) / Strain (production host): STAR
References: UniProt: Q97ZE7, signal-recognition-particle GTPase

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

#3: RNA chain 4.5 S RNA


Mass: 28505.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: signal-recognition-particle GTPase
#5: Protein/peptide DIPEPTIDYL AMINOPEPTIDASE B / DPAP B / YSCV


Mass: 1522.956 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21 (bacteria) / Strain (production host): STAR
References: UniProt: P18962, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases

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Non-polymers , 2 types, 122 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: RNCESPP-SRP-FTSY / Type: RIBOSOME / Details: MICROGRAPHS SELECTED BASED ON CTF
Buffer solutionName: 50 MM HEPES-KOH, 100 MM KOAC, 8 MM MG(OAC)2, PH 7.5 / pH: 7.5
Details: 50 MM HEPES-KOH, 100 MM KOAC, 8 MM MG(OAC)2, PH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN
Details: THE GRIDS WERE PLUNGE FROZEN IN LIQUID ETHANE USING A FEI MARK IV VITRIFICATION ROBOT AFTER BLOTTING FOR 1 S AT RT AND 100 PER CENT RELATIVE HUMIDITY

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jan 11, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 76000 X / Nominal defocus max: 5700 nm / Nominal defocus min: 700 nm / Cs: 2.3 mm
Specimen holderTemperature: 77 K / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 1974

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SINGLE PARTICLE, REFERENCE BASED PROJECTION MATCHINGSingle particle analysis
Resolution: 12 Å / Num. of particles: 46945 / Nominal pixel size: 3.75 Å / Actual pixel size: 3.75 Å / Details: BP RP SUBPROGRAM IN SPIDER / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: FSC / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-ID
11FFH1
21FTS1
33KL41
42XXA1
RefinementHighest resolution: 12 Å
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 1886 1 121 7453

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