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- PDB-4d5l: Cryo-EM structures of ribosomal 80S complexes with termination fa... -
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Basic information
Entry | Database: PDB / ID: 4d5l | |||||||||
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Title | Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus IRES reveal the IRES in the translocated state | |||||||||
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![]() | RIBOSOME / CRPV IRES / TERMINATION / RELEASE FACTORS | |||||||||
Function / homology | ![]() ribosomal subunit / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response ...ribosomal subunit / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | |||||||||
![]() | Muhs, M. / Hilal, T. / Mielke, T. / Skabkin, M.A. / Sanbonmatsu, K.Y. / Pestova, T.V. / Spahn, C.M.T. | |||||||||
![]() | ![]() Title: Cryo-EM of ribosomal 80S complexes with termination factors reveals the translocated cricket paralysis virus IRES. Authors: Margarita Muhs / Tarek Hilal / Thorsten Mielke / Maxim A Skabkin / Karissa Y Sanbonmatsu / Tatyana V Pestova / Christian M T Spahn / ![]() ![]() Abstract: The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the ...The cricket paralysis virus (CrPV) uses an internal ribosomal entry site (IRES) to hijack the ribosome. In a remarkable RNA-based mechanism involving neither initiation factor nor initiator tRNA, the CrPV IRES jumpstarts translation in the elongation phase from the ribosomal A site. Here, we present cryoelectron microscopy (cryo-EM) maps of 80S⋅CrPV-STOP ⋅ eRF1 ⋅ eRF3 ⋅ GMPPNP and 80S⋅CrPV-STOP ⋅ eRF1 complexes, revealing a previously unseen binding state of the IRES and directly rationalizing that an eEF2-dependent translocation of the IRES is required to allow the first A-site occupation. During this unusual translocation event, the IRES undergoes a pronounced conformational change to a more stretched conformation. At the same time, our structural analysis provides information about the binding modes of eRF1 ⋅ eRF3 ⋅ GMPPNP and eRF1 in a minimal system. It shows that neither eRF3 nor ABCE1 are required for the active conformation of eRF1 at the intersection between eukaryotic termination and recycling. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 127.7 KB | Display | |
Data in CIF | ![]() | 224.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2810MC ![]() 2813C ![]() 4d5nC ![]() 4d5yC ![]() 4d61C ![]() 4d67C ![]() 4d66 ![]() 4d68 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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1 |
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Components
-RNA chain , 1 types, 1 molecules 1
#1: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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+40S RIBOSOMAL PROTEIN ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-Details
Sequence details | FOLLOWING HUMAN SEQUENCE USED FOR MODELLING: CHAIN A 1 295 UNP P08865 RSSA_HUMAN 1 295 CHAIN C 1 ...FOLLOWING HUMAN SEQUENCE USED FOR MODELLING: CHAIN A 1 295 UNP P08865 RSSA_HUMAN 1 295 CHAIN C 1 293 UNP P15880 RS2_HUMAN 1 293 CHAIN D 1 243 UNP P23396 RS3_HUMAN 1 243 CHAIN E 1 263 UNP P22090 RS4Y1_HUMAN 1 263 CHAIN I 1 208 UNP P62241 RS8_HUMAN 1 208 CHAIN O 1 151 UNP P62263 RS14_HUMAN 1 151 CHAIN P 1 145 UNP P62841 RS15_HUMAN 1 145 CHAIN R 1 135 UNP P08708 RS17_HUMAN 1 135 CHAIN T 1 145 UNP P39019 RS19_HUMAN 1 145 CHAIN V 1 83 UNP P63220 RS21_HUMAN 1 83 CHAIN Y 1 133 UNP P62847 RS24_HUMAN 1 133 CHAIN a 1 115 UNP P62854 RS26_HUMAN 1 115 CHAIN e 1 59 UNP P62861 RS30_HUMAN 1 59 |
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-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: RIBOSOMAL 80S TERMINATION COMPLEX WITH CRPV IRES-RNA AND ERF1 Type: RIBOSOME / Details: MICROGRAPH SELECTED FOR ASTIGMATISM AND DRIFT |
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Buffer solution | Name: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 2.5 MM MGCL2, 0.5 MM GTP pH: 7.5 Details: 20 MM TRIS PH 7.5, 100 MM KCL, 1 MM DTT, 2.5 MM MGCL2, 0.5 MM GTP |
Specimen | Conc.: 1.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Apr 17, 2012 / Details: MINIMAL DOSE SYSTEM |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 366 |
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Processing
EM software |
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CTF correction | Details: DEFOCUS GROUP | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 9 Å / Num. of particles: 109596 / Nominal pixel size: 1.56 Å / Actual pixel size: 1.56 Å Magnification calibration: CROSS- -CORRELATION DENSITIES WITH REFERENCE STRUCTURE Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2810. (DEPOSITION ID: 12907). 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 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9 Å
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