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Yorodumi- PDB-6f4p: Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f4p | ||||||
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Title | Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM | ||||||
Function / homology | Function and homology information [protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / wybutosine biosynthetic process / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / wybutosine biosynthetic process / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mammalian oogenesis stage / activation-induced cell death of T cells / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / erythrocyte development / Nuclear events stimulated by ALK signaling in cancer / cytosolic ribosome / aminopeptidase activity / gastrulation / methylated histone binding / regulation of signal transduction by p53 class mediator / small-subunit processome / circadian regulation of gene expression / protein destabilization / placenta development / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / rRNA processing / G2/M transition of mitotic cell cycle / p53 binding / glucose homeostasis / chromosome / ribosomal small subunit biogenesis / small ribosomal subunit / cell body / fibroblast proliferation / T cell differentiation in thymus / SARS-CoV-2 modulates host translation machinery / cytosolic small ribosomal subunit / endopeptidase activity / in utero embryonic development / tRNA binding / cytoplasmic translation / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / chromatin binding / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / endoplasmic reticulum / proteolysis / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Chowdhury, R. / Islam, M.S. / Schofield, C.J. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: JMJD5 is a human arginyl C-3 hydroxylase. Authors: Wilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f4p.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f4p.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 6f4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f4p_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 6f4p_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 6f4p_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6f4p_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/6f4p ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f4p | HTTPS FTP |
-Related structure data
Related structure data | 6f4mC 6f4nC 6f4oSC 6f4qC 6f4rC 6f4sC 6f4tC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 29474.092 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 183-416 Source method: isolated from a genetically manipulated source Details: FRAGMENT: 183-416 / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: PNIC28 BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase |
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#2: Protein/peptide | Mass: 1910.385 Da / Num. of mol.: 1 / Fragment: UNP residues 129-144 / Source method: obtained synthetically / Details: FRAGMENT: 129-144 / Source: (synth.) Homo sapiens (human) / References: UniProt: P62753 |
-Non-polymers , 4 types, 332 molecules
#3: Chemical | ChemComp-MN / |
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#4: Chemical | ChemComp-OGA / |
#5: Chemical | ChemComp-TRS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M Bis-Tris pH 6.0, 26.4 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→32.46 Å / Num. obs: 44727 / % possible obs: 98.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4347 / CC1/2: 0.634 / Rpim(I) all: 0.497 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F4O Resolution: 1.45→32.46 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 60.3 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→32.46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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