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- PDB-4ccm: 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ccm | ||||||
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Title | 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1) | ||||||
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![]() | OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / 2- OXOGLUTARATE / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / RPL8 / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING | ||||||
Function / homology | ![]() protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / Protein hydroxylation ...protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / Protein hydroxylation / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of osteoblast differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / cytosolic large ribosomal subunit / postsynapse / cytoplasmic translation / postsynaptic density / rRNA binding / structural constituent of ribosome / iron ion binding / translation / focal adhesion / negative regulation of DNA-templated transcription / nucleolus / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Schofield, C.J. | ||||||
![]() | ![]() Title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E. ...Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J. #1: Journal: Nat.Chem.Biol. / Year: 2012 Title: Oxygenase-Catalyzed Ribosome Hydroxylation Occurs in Prokaryotes and Humans. Authors: Ge, W. / Wolf, A. / Feng, T. / Ho, C. / Sekirnik, R. / Zayer, A. / Granatino, N. / Cockman, M.E. / Loenarz, C. / Loik, N.D. / Hardy, A.P. / Claridge, T.D.W. / Hamed, R.B. / Chowdhury, R. / ...Authors: Ge, W. / Wolf, A. / Feng, T. / Ho, C. / Sekirnik, R. / Zayer, A. / Granatino, N. / Cockman, M.E. / Loenarz, C. / Loik, N.D. / Hardy, A.P. / Claridge, T.D.W. / Hamed, R.B. / Chowdhury, R. / Gong, L. / Robinson, C.V. / Trudgian, D.C. / Jiang, M. / Mackeen, M.M. / Mccullagh, J.S. / Gordiyenko, Y. / Thalhammer, A. / Yamamoto, A. / Yang, M. / Liu-Yi, P. / Zhang, Z. / Schmidt-Zachmann, M. / Kessler, B.M. / Ratcliffe, P.J. / Preston, G.M. / Coleman, M.L. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208 KB | Display | ![]() |
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PDB format | ![]() | 163.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xdvC ![]() 4bu2C ![]() 4bxfC ![]() 4ccjC ![]() 4cckC ![]() 4cclC ![]() 4ccnC ![]() 4ccoC ![]() 4cswC ![]() 4cugC ![]() 4litC ![]() 4liuC ![]() 4livC ![]() 4diqS 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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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 53269.246 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 183-641 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H6W3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen ...References: UniProt: Q9H6W3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor, [histone H3]-dimethyl-L-lysine36 demethylase #2: Protein/peptide | Mass: 3739.275 Da / Num. of mol.: 2 / Fragment: RESIDUES 205-239 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 356 molecules ![](data/chem/img/MN.gif)
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.66 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M BIS-TRIS PROPANE PH 6.8, 0.25M MAGNESIUM FORMATE, 0.002M MNCL2, TEMPERATURE 293K VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 / 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: 2.51→44.07 Å / Num. obs: 41312 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.51→2.58 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4DIQ Resolution: 2.51→44.07 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 268067.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.3454 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.51→44.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.51→2.58 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 12
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Xplor file |
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