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Yorodumi- PDB-8tpu: Subtomogram averaged consensus structure of the malarial 80S ribo... -
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-Basic information
Entry | Database: PDB / ID: 8tpu | ||||||||||||
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Title | Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes | ||||||||||||
Components |
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Keywords | RIBOSOME / malaria / cryoET / in situ / Plasmodium falciparum / translation | ||||||||||||
Function / homology | Function and homology information RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs ...RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) / Iron uptake and transport / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Negative regulators of DDX58/IFIH1 signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Aggrephagy / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / 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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome binding / kinase activity / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / ubiquitin-dependent protein catabolic process / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Anton, L. / Cheng, W. / Zhu, X. / Ho, C.M. | ||||||||||||
Funding support | United States, Switzerland, France, 3items
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Citation | Journal: To Be Published Title: Divergent translational landscape reflects adaptation to biased codon usage in malaria parasites Authors: Anton, L. / Cheng, W. / Haile, M. / Cobb, D.W. / Zhu, X. / Han, L. / Li, E. / Nair, A. / Lee, C.L. / Ho, C.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tpu.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tpu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tpu_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8tpu_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8tpu_validation.xml.gz | 290.9 KB | Display | |
Data in CIF | 8tpu_validation.cif.gz | 530.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/8tpu ftp://data.pdbj.org/pub/pdb/validation_reports/tp/8tpu | HTTPS FTP |
-Related structure data
Related structure data | 41485MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+40S ribosomal protein ... , 29 types, 29 molecules S1S2S3S4SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZ
+60S ribosomal protein ... , 39 types, 39 molecules S5S7ALA1A2A4A6A7ANA8A9AaAbAdAeAIAJAKAMASAOAQARAWAYATAZA3A5AD...
-Protein/peptide , 1 types, 1 molecules S6
#6: Protein/peptide | Mass: 4925.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O96269 |
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-RNA chain , 4 types, 4 molecules SAAAACAB
#8: RNA chain | Mass: 669744.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1013064538 |
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#34: RNA chain | Mass: 1216212.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) |
#35: RNA chain | Mass: 51206.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1162436939 |
#36: RNA chain | Mass: 38410.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) |
-Protein , 2 types, 2 molecules AfS8
#50: Protein | Mass: 14645.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ID50 |
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#79: Protein | Mass: 35726.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBA0 |
-Ribosomal protein ... , 2 types, 2 molecules APAc
#51: Protein | Mass: 23985.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) |
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#56: Protein | Mass: 10571.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4L5 |
-Large ribosomal subunit protein ... , 2 types, 2 molecules AhAi
#52: Protein | Mass: 10755.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) |
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#53: Protein | Mass: 12065.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Plasmodium falciparum 80S ribosome consensus structure Type: RIBOSOME Details: Subtomogram averaged consensus structure of the malarial 80S ribosome in Plasmodium falciparum-infected human erythrocytes Entity ID: #1-#4, #51-#75, #5-#8 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 2800 nm |
Image recording | Electron dose: 2.93 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 500.24002 Å / B: 500.24002 Å / C: 500.24002 Å / Space group name: C1 / Space group num: 1 | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120226 / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 848 / Num. of volumes extracted: 129617 | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 136.19 Å2 | ||||||||||||||||||||||||
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