+Open data
-Basic information
Entry | Database: PDB / ID: 2xkv | |||||||||
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Title | Atomic Model of the SRP-FtsY Early Conformation | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity ...endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å | |||||||||
Authors | Estrozi, L.F. / Boehringer, D. / Shan, S.-o. / Ban, N. / Schaffitzel, C. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2xkv.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xkv.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xkv_validation.pdf.gz | 816.1 KB | Display | wwPDB validaton report |
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Full document | 2xkv_full_validation.pdf.gz | 826.9 KB | Display | |
Data in XML | 2xkv_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2xkv_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xkv ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xkv | HTTPS FTP |
-Related structure data
Related structure data | 1762MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: RNA chain | 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 | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RNC-SRP-FTSY / Type: RIBOSOME |
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Buffer solution | pH: 7.5 / Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Image recording | Film or detector model: KODAK SO-163 FILM |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 13.5 Å / Num. of particles: 28822 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Space: REAL | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 13.5 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 13.5 Å
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