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- PDB-9fxo: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SIT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9fxo | ||||||||||||||||||
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Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT | ||||||||||||||||||
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![]() | RIBOSOME / CRYO-EM / LEISHMANIA MAJOR / 80S RIBOSOME / TRNA / MRNA / snoRNA | ||||||||||||||||||
Function / homology | ![]() ciliary transition zone / ciliary plasm / nuclear lumen / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome ...ciliary transition zone / ciliary plasm / nuclear lumen / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / kinase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å | ||||||||||||||||||
![]() | Rajan, K.S. / Yonath, A. | ||||||||||||||||||
Funding support | European Union, 1items
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![]() | ![]() Title: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT Authors: Rajan, K.S. / Yonath, A. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 6.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 388.9 KB | Display | |
Data in CIF | ![]() | 663.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 50852MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+RNA chain , 12 types, 13 molecules L1L2L3L4L5L6L7L8S1S2S4S3S5
+Putative 60S ... , 23 types, 23 molecules LALELFLHLILJLLLNLOLQLSLTLULVLWLZLaLcLeLhLiLlLp
+Putative ribosomal protein ... , 7 types, 7 molecules LBLCLXLgLkSMSS
+60S ribosomal protein ... , 9 types, 9 molecules LDLGLPLRLYLbLdLfLo
+Putative 40S ribosomal protein ... , 15 types, 15 molecules LKSCSDSJSLSNSPSRSTSUSVSWSYScSd
+Ribosomal protein ... , 3 types, 3 molecules LMLjLn
+Ubiquitin-60S ribosomal protein ... , 2 types, 2 molecules LmSf
+40S ribosomal protein ... , 15 types, 15 molecules SASBSESFSGSHSISKSOSQSXSZSaSbSe
+Protein , 2 types, 2 molecules SgSh
+Non-polymers , 8 types, 3259 molecules 














+Details
-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: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT Type: RIBOSOME / Entity ID: #3-#4, #6-#51, #54-#87 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 0.92 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150124 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.73 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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