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Yorodumi- PDB-8hky: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hky | ||||||
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Title | Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome | ||||||
Components |
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Keywords | RIBOSOME / Sulfolobus acidocaldarius ribosome | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius DSM 639 (acidophilic) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.45 Å | ||||||
Authors | Wang, Y.H. / Zhou, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome Authors: Wang, Y.H. / Zhou, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hky.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8hky.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8hky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/8hky ftp://data.pdbj.org/pub/pdb/validation_reports/hk/8hky | HTTPS FTP |
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-Related structure data
Related structure data | 34863MC 8hkuC 8hkvC 8hkxC 8hl4C 8hl5C 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
-RNA chain , 5 types, 7 molecules A23SA16SAATNAPTNAETNA5SAMRN
#1: RNA chain | Mass: 980552.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) | ||||
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#2: RNA chain | Mass: 487531.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) | ||||
#3: RNA chain | Mass: 24485.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) #4: RNA chain | | Mass: 39440.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) References: GenBank: 68566501 #67: RNA chain | | Mass: 2710.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) |
+50S ribosomal protein ... , 34 types, 37 molecules AL1PAL2PAL3PAL4PAL5PAL6PALX0L10EL13PL141L142L14PL15EL18EL18PL19EL22PL23PL24EL24PL29PL30EL30PL31EL32EL34EL37AL37EL39EL40E...
-Protein , 2 types, 2 molecules L45AL46A
#38: Protein | Mass: 11662.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) References: UniProt: Q4J9G6 |
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#39: Protein | Mass: 8320.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) References: UniProt: Q4J953 |
+30S ribosomal protein ... , 25 types, 25 molecules AS2PAS4EAS4PAS5PAS6EAS8EAS8PS11PS12PS15PS17PS24ES27ES3AEAS3PAS7PS10PS13PS14PS17ES19ES19PAS9PS28ES27A
-Protein/peptide / Non-polymers , 2 types, 58 molecules APTP
#66: Protein/peptide | Mass: 901.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic) |
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#68: Chemical | ChemComp-UNK / |
-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: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Sulfolobus acidocaldarius ribosome / Type: RIBOSOME / Entity ID: #1-#67 / Source: NATURAL |
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Source (natural) | Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 26.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5781 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 319.32 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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