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Yorodumi- PDB-8pu0: Cryo-EM structure of human Elp123 in complex with tRNA, desulpho-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pu0 | ||||||
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Title | Cryo-EM structure of human Elp123 in complex with tRNA, desulpho-CoA, 5'-deoxyadenosine and methionine | ||||||
Components |
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Keywords | TRANSLATION / Elongator / tRNA modification / acetyl-CoA hydrolysis | ||||||
Function / homology | Function and homology information phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription elongation factor complex / central nervous system development ...phosphorylase kinase regulator activity / tRNA uridine(34) acetyltransferase activity / elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of receptor signaling pathway via JAK-STAT / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription elongation factor complex / central nervous system development / transcription elongation by RNA polymerase II / neuron migration / : / regulation of translation / 4 iron, 4 sulfur cluster binding / HATs acetylate histones / tRNA binding / positive regulation of cell migration / nucleolus / regulation of transcription by RNA polymerase II / protein kinase binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å | ||||||
Authors | Abbassi, N. / Jaciuk, M. / Lin, T.-Y. / Glatt, S. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human Elp123 in complex with tRNA, desulpho-CoA, 5'-deoxyadenosine and methionine Authors: Abbassi, N. / Jaciuk, M. / Lin, T.-Y. / Glatt, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pu0.cif.gz | 534.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pu0.ent.gz | 411.5 KB | Display | PDB format |
PDBx/mmJSON format | 8pu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/8pu0 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/8pu0 | HTTPS FTP |
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-Related structure data
Related structure data | 17927MC 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
-Elongator complex protein ... , 3 types, 4 molecules AEBC
#1: Protein | Mass: 150427.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELP1, IKAP, IKBKAP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95163 #2: Protein | | Mass: 92597.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELP2, STATIP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6IA86 #3: Protein | | Mass: 65740.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELP3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9H9T3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-RNA chain , 1 types, 1 molecules X
#4: RNA chain | Mass: 24047.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 4 molecules
#5: Chemical | ChemComp-DCA / |
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#6: Chemical | ChemComp-SF4 / |
#7: Chemical | ChemComp-5AD / |
#8: Chemical | ChemComp-MET / |
-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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human Elp123 in complex with glutamine tRNA, desulpho-CoA, 5'-deoxyadenosine and methionine Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.635 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: spodoptera frugiperda (fall armyworm) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 8 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 15 s wait time, blot force 5, 5 s blot time |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 41.22 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 20720 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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Image processing | Details: 20 eV slit, fully tuned before the experiment | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115026 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: Elp123-tRNA-ACO structure from the same study / Source name: Other / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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