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Yorodumi- PDB-4v4n: Structure of the Methanococcus jannaschii ribosome-SecYEBeta chan... -
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-Basic information
Entry | Database: PDB / ID: 4v4n | |||||||||
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Title | Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex | |||||||||
Components |
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Keywords | RIBOSOME/PROTEIN TRANSPORT / archaea / archaeal / ribosomal / 50S / protein synthesis / RNA / large subunit / co-translational translocation / protein conducting channel / RIBOSOME-PROTEIN TRANSPORT 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 | Methanococcus jannaschii (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | |||||||||
Authors | Menetret, J.F. / Park, E. / Gumbart, J.C. / Ludtke, S.J. / Li, W. / Whynot, A. / Rapoport, T.A. / Akey, C.W. | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Structure of the SecY channel during initiation of protein translocation. Authors: Eunyong Park / Jean-François Ménétret / James C Gumbart / Steven J Ludtke / Weikai Li / Andrew Whynot / Tom A Rapoport / Christopher W Akey / Abstract: Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during ...Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome-nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome-channel complexes with cryo-electron microscopy. Non-translating ribosome-SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome-channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly. | |||||||||
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 | 4v4n.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v4n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v4n_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4v4n_full_validation.pdf.gz | 6 MB | Display | |
Data in XML | 4v4n_validation.xml.gz | 735.5 KB | Display | |
Data in CIF | 4v4n_validation.cif.gz | 1 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v4n ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4n | HTTPS FTP |
-Related structure data
Related structure data | 5691MC 5692C 5693C 3j45C 3j46C 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
-Preprotein translocase subunit ... , 2 types, 2 molecules A7A8
#1: Protein | Mass: 7701.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q57817 |
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#2: Protein | Mass: 5853.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P60460 |
+50S ribosomal protein ... , 34 types, 35 molecules AfAQASATAUAWA5AKAAAaABAbACADAdAEAeAFAgAHAhAIAiAJAjAkALAMANAO...
-Protein , 1 types, 1 molecules AX
#9: Protein | Mass: 47482.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus jannaschii (archaea) / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q60175 |
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-RNA chain , 4 types, 4 molecules B1B2A1A3
#10: RNA chain | Mass: 24880.865 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea) |
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#11: RNA chain | Mass: 485455.500 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea) |
#38: RNA chain | Mass: 990820.375 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea) |
#39: RNA chain | Mass: 40689.262 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Methanococcus jannaschii (archaea) |
+30S ribosomal protein ... , 26 types, 27 molecules B3AGBABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBY
-Details
Sequence details | RIBOSOME COORDINATE |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY / Number of used crystals: 1 |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 2.6 MDa / Experimental value: NO | |||||||||||||||||||||||||
Buffer solution | Name: 100 mM NH4Cl, 30 mM MgCl2, 20 mM HEPES-KOH, 6 mM beta-mercaptoethanol, 0.1% DDM pH: 7.5 Details: 100 mM NH4Cl, 30 mM MgCl2, 20 mM HEPES-KOH, 6 mM beta-mercaptoethanol, 0.1% DDM | |||||||||||||||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: Quantifoil 400 mesh 2/1 Cu grids, air glow discharged, and 400 mesh Cu grids with a thin continuous carbon foil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 77 K / Humidity: 100 % Details: Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Apr 10, 2008 / Details: Low dose imaging, data collected manually |
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: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Oxford holder / Temperature: 93 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM / Details: Kodak SO163 film |
Image scans | Num. digital images: 217 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: per micrograph | ||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: projection matching / Resolution: 9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37000 / Nominal pixel size: 2.73 Å / Actual pixel size: 2.73 Å Details: Final map calculated as an average of 6 different refinements in EMAN2 with different parameters. Resolution method was FSC at 0.5 cut-off using a comparison between experimental map and a ...Details: Final map calculated as an average of 6 different refinements in EMAN2 with different parameters. Resolution method was FSC at 0.5 cut-off using a comparison between experimental map and a map of the docked ribosomal models calculated at 7 Angstrom resolution with EMAN. Num. of class averages: 3800 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building | Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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