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- PDB-4ccm: 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex ... -

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Basic information

Entry
Database: PDB / ID: 4ccm
Title60S 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)
Components
  • 60S RIBOSOMAL PROTEIN L8
  • BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
KeywordsOXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / 2- OXOGLUTARATE / DIOXYGENASE / JMJC DOMAIN / RIBOSOME BIOGENESIS / NUCLEAR PROTEIN / RPL8 / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING
Function / homology
Function and homology information


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 / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of osteoblast differentiation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / Regulation of expression of SLITs and ROBOs / cytosolic large ribosomal subunit / cytoplasmic translation / postsynapse / postsynaptic density / rRNA binding / structural constituent of ribosome / translation / iron ion binding / focal adhesion / negative regulation of DNA-templated transcription / nucleolus / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal oxygenase 1, C-terminal winged helix domain / JmjC domain-containing ribosomal oxygenase (ROX), dimer domain / Outer Surface Protein A; domain 3 - #40 / JmjC domain-containing / JmjC domain / Outer Surface Protein A; domain 3 / Ribosomal protein L2, archaeal-type / Cupin / JmjC domain ...: / Ribosomal oxygenase 1, C-terminal winged helix domain / JmjC domain-containing ribosomal oxygenase (ROX), dimer domain / Outer Surface Protein A; domain 3 - #40 / JmjC domain-containing / JmjC domain / Outer Surface Protein A; domain 3 / Ribosomal protein L2, archaeal-type / Cupin / JmjC domain / JmjC domain profile. / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L2, domain 3 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal Proteins L2, RNA binding domain / Translation protein SH3-like domain superfamily / Arc Repressor Mutant, subunit A / Ribosomal protein L2, domain 2 / Jelly Rolls / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Large ribosomal subunit protein uL2 / Ribosomal oxygenase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChowdhury, R. / Schofield, C.J.
Citation
Journal: Nature / Year: 2014
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
DepositionOct 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
B: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
C: 60S RIBOSOMAL PROTEIN L8
D: 60S RIBOSOMAL PROTEIN L8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,60711
Polymers114,0174
Non-polymers5907
Water6,287349
1
A: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
B: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
C: 60S RIBOSOMAL PROTEIN L8
D: 60S RIBOSOMAL PROTEIN L8
hetero molecules

A: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
B: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66
C: 60S RIBOSOMAL PROTEIN L8
D: 60S RIBOSOMAL PROTEIN L8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,21522
Polymers228,0348
Non-polymers1,18114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area27360 Å2
ΔGint-137.4 kcal/mol
Surface area70230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.770, 83.500, 96.870
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL-HYDROXYLASE NO66 / 60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE / HISTONE LYSINE DEMETHYLASE NO66 / MYC-ASSOCIATED ...60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE / HISTONE LYSINE DEMETHYLASE NO66 / MYC-ASSOCIATED PROTEIN WITH JMJC DOMAIN / NUCLEOLAR PROTEIN 66 / HSNO66 / RIBOSOMAL OXYGENASE NO66 / ROX


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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
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 60S RIBOSOMAL PROTEIN L8 /


Mass: 3739.275 Da / Num. of mol.: 2 / Fragment: RESIDUES 205-239 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P62917

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Non-polymers , 4 types, 356 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.66 % / Description: NONE
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
CNS1.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DIQ

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
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2091 5 %RANDOM
Rwork0.228 ---
obs0.228 41312 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.3454 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1--18.68 Å20 Å21.36 Å2
2--17.23 Å20 Å2
3---1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.51→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7445 0 34 349 7828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.51→2.58 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.386 146 4.8 %
Rwork0.372 3024 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4OGA.PAROGA.TOP
X-RAY DIFFRACTION5EDO.PAREDO.TOP

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