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- PDB-2xkv: Atomic Model of the SRP-FtsY Early Conformation -

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Basic information

Entry
Database: PDB / ID: 2xkv
TitleAtomic Model of the SRP-FtsY Early Conformation
Components
  • (SIGNAL RECOGNITION PARTICLE PROTEIN) x 2
  • 4.5S RNA
  • CELL DIVISION PROTEIN FTSY
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane ...signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytosol / cytoplasm
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 / 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 protein / Signal recognition particle protein / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsEstrozi, L.F. / Boehringer, D. / Shan, S.-o. / Ban, N. / Schaffitzel, C.
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor.
Authors: Leandro F Estrozi / Daniel Boehringer / Shu-Ou Shan / Nenad Ban / Christiane Schaffitzel /
Abstract: We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the ...We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the tetraloop of the SRP RNA, whereas the NG domains of the SRP protein and FtsY interact weakly in this conformation. Our results suggest that optimal positioning of the SRP RNA tetraloop and the Ffh NG domain leads to FtsY recruitment.
History
DepositionJul 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Version format compliance
Revision 1.2Mar 20, 2013Group: Other / Refinement description
Revision 2.0Aug 23, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / entity / entity_src_gen / entity_src_nat / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.fitting_id / _em_software.image_processing_id / _entity.src_method

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: 4.5S RNA
C: SIGNAL RECOGNITION PARTICLE PROTEIN
D: CELL DIVISION PROTEIN FTSY


Theoretical massNumber of molelcules
Total (without water)110,2904
Polymers110,2904
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: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / / FIFTY-FOUR HOMOLOG


Mass: 32300.371 Da / Num. of mol.: 1 / Fragment: NG DOMAIN, RESIDUES 1-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O07347, signal-recognition-particle GTPase
#2: RNA chain 4.5S RNA


Mass: 36856.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ONLY THE PART OF THE 4.5S RNA THAT IS VISIBLE IN THE EM RECONSTRUCTION IS INCLUDED
Source: (natural) ESCHERICHIA COLI (E. coli)
#3: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / / FIFTY-FOUR HOMOLOG / P48


Mass: 8160.762 Da / Num. of mol.: 1 / Fragment: M DOMAIN, RESIDUES 329-430 / Source method: isolated from a natural source
Details: ONLY THE PART OF THE M DOMAIN THAT IS VISIBLE IN THE EM RECONSTRUCTION IS INCLUDED
Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P0AGD7
#4: Protein CELL DIVISION PROTEIN FTSY /


Mass: 32972.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P83749

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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: RNC-SRP-FTSY / Type: RIBOSOME
Buffer solutionpH: 7.5 / Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1CNSmodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 13.5 Å / Num. of particles: 28822 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
11DUL1
21OKK1
RefinementHighest resolution: 13.5 Å
Refinement stepCycle: LAST / Highest resolution: 13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 2050 0 0 6620

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