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Yorodumi- PDB-3dkn: Sec61 in the Canine ribosome-channel complex from the endoplasmic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dkn | ||||||
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Title | Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum | ||||||
Components |
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Keywords | protein transport/RNA / Ribosome-channel complex / co-translational translocation / endoplasmic reticulum / protein transport-RNA COMPLEX | ||||||
Function / homology | Function and homology information intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å | ||||||
Authors | Menetret, J.-F. / Akey, C. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Authors: Jean-François Ménétret / Ramanujan S Hegde / Mike Aguiar / Steven P Gygi / Eunyong Park / Tom A Rapoport / Christopher W Akey / Abstract: During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we ...During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures. | ||||||
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 | 3dkn.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dkn.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dkn_validation.pdf.gz | 811.2 KB | Display | wwPDB validaton report |
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Full document | 3dkn_full_validation.pdf.gz | 898.9 KB | Display | |
Data in XML | 3dkn_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 3dkn_validation.cif.gz | 50.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dkn ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dkn | HTTPS FTP |
-Related structure data
Related structure data | 1528MC 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
-RNA chain , 3 types, 3 molecules DEF
#1: RNA chain | Mass: 6421.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: helix 6 / Source: (natural) Canis lupus familiaris (dog) |
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#2: RNA chain | Mass: 5543.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: helix 7 / Source: (natural) Canis lupus familiaris (dog) |
#3: RNA chain | Mass: 10289.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: helix 50 / Source: (natural) Canis lupus familiaris (dog) |
-Preprotein translocase subunit ... , 3 types, 3 molecules ABC
#4: Protein | Mass: 46736.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q60175*PLUS |
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#5: Protein | Mass: 7440.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q57817*PLUS |
#6: Protein/peptide | Mass: 3639.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P60460*PLUS |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | Name: 30mM Hepes 50mM KAc, 10mM Mg acetate and 1.5% digitonin. pH: 7.5 Details: 30mM Hepes 50mM KAc, 10mM Mg acetate and 1.5% digitonin. | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Details: continuous thin carbon on 400 mesh copper grids | ||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Home-made plunger |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jul 27, 2001 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 51000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: per micrograph | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: projection matching with EMAN / Resolution: 8.7 Å / Num. of particles: 79000 / Actual pixel size: 2.73 Å / Magnification calibration: vermiculite crystals Details: 8.7 angstrom resolution for the 80S ribosome, 11.1 angstrom resolution for the Sec61 region of the channel density Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--Rigid body, then local flexible fitting | |||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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