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- PDB-6f4q: Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f4q | ||||||
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Title | Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2) | ||||||
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![]() | 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 | ![]() [protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / 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 / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / L13a-mediated translational silencing of Ceruloplasmin expression / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nuclear events stimulated by ALK signaling in cancer / aminopeptidase activity / cytosolic ribosome / 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 / rRNA processing / G1/S transition of mitotic cell cycle / 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 / cytoplasmic translation / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / dendrite / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / endoplasmic reticulum / proteolysis / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Islam, M.S. / Schofield, C.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.7 KB | Display | ![]() |
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PDB format | ![]() | 144.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6f4mC ![]() 6f4nC ![]() 6f4oC ![]() 6f4pSC ![]() 6f4rC ![]() 6f4sC ![]() 6f4tC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 29449.107 Da / Num. of mol.: 1 / Mutation: C217A, C232A, Q275C, C295A, C384A Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN (RESIDUES 183-416) / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase |
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#2: Protein/peptide | Mass: 1942.450 Da / Num. of mol.: 1 / Mutation: A138C / Source method: obtained synthetically / Details: FRAGMENT: 129-144 / Source: (synth.) ![]() |
-Non-polymers , 5 types, 366 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / | ||
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#4: Chemical | ChemComp-OGA / | ||
#5: Chemical | ChemComp-TRS / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M Bis-Tris pH 6.0, 19.3 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2016 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→49.91 Å / Num. obs: 95694 / % possible obs: 98.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.1 / Num. unique obs: 9219 / CC1/2: 0.707 / Rpim(I) all: 0.411 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6F4P Resolution: 1.12→49.907 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.03 Details: REFINEMENT TARGET: ML and BULK SOLVENT MODELLING METHOD USED: FLAT MODEL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 54.5 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.12→49.907 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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