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- PDB-2iy3: Structure of the E. Coli Signal Regognition Particle -

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Basic information

Entry
Database: PDB / ID: 2iy3
TitleStructure of the E. Coli Signal Regognition Particle
Components
  • 4.5S RNA
  • SIGNAL SEQUENCE
  • Signal recognition particle protein,Signal recognition particle 54 kDa protein
KeywordsRNA-BINDING / RNA-BINDING PROTEIN COMPLEX / SIGNAL RECOGNITION PARTICLE
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
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 ...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 / 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 54 kDa protein / Signal recognition particle protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Sulfolobus solfataricus (archaea)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å
Model type detailsCA ATOMS ONLY, CHAIN A, C ; P ATOMS ONLY, CHAIN B
AuthorsSchaffitzel, C. / Oswald, M. / Berger, I. / Ishikawa, T. / Abrahams, J.P. / Koerten, H.K. / Koning, R.I. / Ban, N.
CitationJournal: Nature / Year: 2006
Title: Structure of the E. coli signal recognition particle bound to a translating ribosome.
Authors: Christiane Schaffitzel / Miro Oswald / Imre Berger / Takashi Ishikawa / Jan Pieter Abrahams / Henk K Koerten / Roman I Koning / Nenad Ban /
Abstract: The prokaryotic signal recognition particle (SRP) targets membrane proteins into the inner membrane. It binds translating ribosomes and screens the emerging nascent chain for a hydrophobic signal ...The prokaryotic signal recognition particle (SRP) targets membrane proteins into the inner membrane. It binds translating ribosomes and screens the emerging nascent chain for a hydrophobic signal sequence, such as the transmembrane helix of inner membrane proteins. If such a sequence emerges, the SRP binds tightly, allowing the SRP receptor to lock on. This assembly delivers the ribosome-nascent chain complex to the protein translocation machinery in the membrane. Using cryo-electron microscopy and single-particle reconstruction, we obtained a 16 A structure of the Escherichia coli SRP in complex with a translating E. coli ribosome containing a nascent chain with a transmembrane helix anchor. We also obtained structural information on the SRP bound to an empty E. coli ribosome. The latter might share characteristics with a scanning SRP complex, whereas the former represents the next step: the targeting complex ready for receptor binding. High-resolution structures of the bacterial ribosome and of the bacterial SRP components are available, and their fitting explains our electron microscopic density. The structures reveal the regions that are involved in complex formation, provide insight into the conformation of the SRP on the ribosome and indicate the conformational changes that accompany high-affinity SRP binding to ribosome nascent chain complexes upon recognition of the signal sequence.
History
DepositionJul 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2006Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Aug 23, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id

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Assembly

Deposited unit
A: Signal recognition particle protein,Signal recognition particle 54 kDa protein
B: 4.5S RNA
C: SIGNAL SEQUENCE


Theoretical massNumber of molelcules
Total (without water)85,2023
Polymers85,2023
Non-polymers00
Water0
1


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

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Components

#1: Protein Signal recognition particle protein,Signal recognition particle 54 kDa protein / / Fifty-four homolog / SRP54 / Coordinate model: Cα atoms only


Mass: 48274.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria), (gene. exp.) Sulfolobus solfataricus (archaea)
Gene: ffh, srp54, SULA_1982, SULB_1983, SULC_1981 / Plasmid: PET24A_FFH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O07347, UniProt: A0A0E3MG81
#2: RNA chain 4.5S RNA / Coordinate model: P atoms only


Mass: 35547.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1126835767
#3: Protein/peptide SIGNAL SEQUENCE / / Coordinate model: Cα atoms only


Mass: 1380.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct

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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: SRP BOUND TO RIBOSOME / Type: RIBOSOME
Buffer solutionName: 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 1 MM DTT,1 MM GTP
pH: 7.5
Details: 50 MM HEPES-KOH PH 7.5, 100 MM KCL, 25 MM MGCL2, 1 MM DTT,1 MM GTP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20 / Date: Jun 2, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTemperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 251

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Processing

EM software
IDNameCategory
1NOMADmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPING
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 16 Å / Num. of particles: 24382 / Nominal pixel size: 3.81 Å
Details: THE COORDINATES BELOW ARE MADE UP FROM THE FOLLOWING COMPONENTS: FFH NG DOMAIN (RESIDUE 1-296), ORGANISM SCIENTIFIC: THERMUS AQUATICUS (PDB ENTRY 1JPN CHAIN A). FFH M DOMAIN (RESIDUE 297-432) ...Details: THE COORDINATES BELOW ARE MADE UP FROM THE FOLLOWING COMPONENTS: FFH NG DOMAIN (RESIDUE 1-296), ORGANISM SCIENTIFIC: THERMUS AQUATICUS (PDB ENTRY 1JPN CHAIN A). FFH M DOMAIN (RESIDUE 297-432), ORANISM SCIENTIFIC: SULFOLOBUS SOLFATARICUS (PDB ENTRY 1QZW CHAIN A). 4.5S RNA (RESIDUE 33- 73), ORGANISM SCIENTIFIC: SULFOLOBUS SOLFATARICUS (PDB ENTRY 1QZW, CHAIN B). 4.5S RNA (RESIDUE 1-32 AND 74-110), ORGANISM SCIENTIFIC: ESCHERICHIA COLI (PDB: SRPDB, ROSENBLAD ET AL, NUCLEIC ACID RES 21, 363-364,12:2003.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY
Atomic model building
IDPDB-ID 3D fitting-ID
11JPN

1jpn

1
21QZW

1qzw

1
RefinementHighest resolution: 16 Å
Refinement stepCycle: LAST / Highest resolution: 16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms449 110 0 0 559

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