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- PDB-4ujc: mammalian 80S HCV-IRES initiation complex with eIF5B POST-like state -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ujc | ||||||||||||
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Title | mammalian 80S HCV-IRES initiation complex with eIF5B POST-like state | ||||||||||||
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![]() | RIBOSOME / TRANSLATION INITIATION / HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE / EUKARYOTIC INITIATION FACTOR 5B | ||||||||||||
Function / homology | ![]() translation initiation factor activity / GTPase activity / GTP binding / mitochondrion Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | ||||||||||||
![]() | Yamamoto, H. / Unbehaun, A. / Loerke, J. / Behrmann, E. / Marianne, C. / Burger, J. / Mielke, T. / Spahn, C.M.T. | ||||||||||||
![]() | ![]() Title: Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA. Authors: Hiroshi Yamamoto / Anett Unbehaun / Justus Loerke / Elmar Behrmann / Marianne Collier / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / ![]() Abstract: The universally conserved eukaryotic initiation factor (eIF) 5B, a translational GTPase, is essential for canonical translation initiation. It is also required for initiation facilitated by the ...The universally conserved eukaryotic initiation factor (eIF) 5B, a translational GTPase, is essential for canonical translation initiation. It is also required for initiation facilitated by the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) RNA. eIF5B promotes joining of 60S ribosomal subunits to 40S ribosomal subunits bound by initiator tRNA (Met-tRNAi(Met)). However, the exact molecular mechanism by which eIF5B acts has not been established. Here we present cryo-EM reconstructions of the mammalian 80S-HCV-IRES-Met-tRNAi(Met)-eIF5B-GMPPNP complex. We obtained two substates distinguished by the rotational state of the ribosomal subunits and the configuration of initiator tRNA in the peptidyl (P) site. Accordingly, a combination of conformational changes in the 80S ribosome and in initiator tRNA facilitates binding of the Met-tRNAi(Met) to the 60S P site and redefines the role of eIF5B as a tRNA-reorientation factor. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 334.8 KB | Display | |
Data in CIF | ![]() | 607 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2683MC ![]() 2682C ![]() 4ujdC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 6 types, 6 molecules AAACA2A3A4C1
#1: RNA chain | Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: RNA chain | Mass: 162190.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: RNA chain | Mass: 1625917.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: RNA chain | Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#50: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules ABBm
#2: Protein | Mass: 70788.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#44: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+60S RIBOSOMAL PROTEIN ... , 42 types, 42 molecules BABBBCBDBEBFBGBHBIBJBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBe...
+40S RIBOSOMAL PROTEIN ... , 33 types, 33 molecules CACBCCCDCECFCGCHCICJCKCLCMCNCOCPCQCRCSCTCUCVCWCXCYCZCaCbCcCd...
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#84: Chemical | ChemComp-GNP / |
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#85: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: HCV-IRES 80S INITIATION COMPLEX WITH EIF5B POST- LIKE STATE Type: RIBOSOME |
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Buffer solution | Name: 20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT pH: 7.6 Details: 20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK I, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING, |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Dec 22, 2012 / Details: AUTOMATED DATA COLLECTION USING LEGINON |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 115000 X / Calibrated magnification: 194805 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: CTFFIND3 | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 9.5 Å / Num. of particles: 541570 / Nominal pixel size: 2.37 Å / Actual pixel size: 2.37 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2683. (DEPOSITION ID: 12564). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 4CXC![]() 4cxc | ||||||||||||
Refinement | Highest resolution: 9.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9.5 Å
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