[English] 日本語
Yorodumi- PDB-4ujc: mammalian 80S HCV-IRES initiation complex with eIF5B POST-like state -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ujc | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | mammalian 80S HCV-IRES initiation complex with eIF5B POST-like state | ||||||||||||
Components |
| ||||||||||||
Keywords | RIBOSOME / TRANSLATION INITIATION / HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE / EUKARYOTIC INITIATION FACTOR 5B | ||||||||||||
Function / homology | Function and homology information translation initiation factor activity / GTPase activity / GTP binding / mitochondrion Similarity search - Function | ||||||||||||
Biological species | ORYCTOLAGUS CUNICULUS (rabbit) HEPATITIS C VIRUS | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | ||||||||||||
Authors | Yamamoto, H. / Unbehaun, A. / Loerke, J. / Behrmann, E. / Marianne, C. / Burger, J. / Mielke, T. / Spahn, C.M.T. | ||||||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2014 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4ujc.cif.gz | 4.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ujc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4ujc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ujc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ujc_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4ujc_validation.xml.gz | 334.8 KB | Display | |
Data in CIF | 4ujc_validation.cif.gz | 607 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/4ujc ftp://data.pdbj.org/pub/pdb/validation_reports/uj/4ujc | HTTPS FTP |
-Related structure data
Related structure data | 2683MC 2682C 4ujdC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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) ORYCTOLAGUS CUNICULUS (rabbit) |
---|---|
#3: RNA chain | Mass: 162190.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HEPATITIS C VIRUS |
#4: RNA chain | Mass: 1625917.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) |
#5: RNA chain | Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) |
#6: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) |
#50: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) |
-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) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TRL5 |
---|---|
#44: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) |
+60S RIBOSOMAL PROTEIN ... , 42 types, 42 molecules BABBBCBDBEBFBGBHBIBJBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBe...
+40S RIBOSOMAL PROTEIN ... , 33 types, 33 molecules CACBCCCDCECFCGCHCICJCKCLCMCNCOCPCQCRCSCTCUCVCWCXCYCZCaCbCcCd...
-Non-polymers , 2 types, 2 molecules
#84: Chemical | ChemComp-GNP / |
---|---|
#85: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: HCV-IRES 80S INITIATION COMPLEX WITH EIF5B POST- LIKE STATE Type: RIBOSOME |
---|---|
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, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F30 / Date: Dec 22, 2012 / Details: AUTOMATED DATA COLLECTION USING LEGINON |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|