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- PDB-4y3o: Crystal structure of Ribosomal oxygenase NO66 in complex with sub... -

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Basic information

Entry
Database: PDB / ID: 4y3o
TitleCrystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine
Components
  • Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66
  • Rpl8 peptide
KeywordsOXIDOREDUCTASE/PEPTIDE / Ribosomal oxygenase / Quaternary compound structure / JMJC-domain / OXIDOREDUCTASE-PEPTIDE complex
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 / 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 / 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 / postsynapse / cytosolic large ribosomal subunit / cytoplasmic translation / 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 signature. / Ribosomal protein L2, conserved site / 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 Proteins L2, RNA binding domain / Ribosomal protein L2 / 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
ACETATE ION / NICKEL (II) ION / N-OXALYLGLYCINE / Large ribosomal subunit protein uL2 / Ribosomal oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWang, C. / Zhang, Q. / Zang, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
Authors: Wang, C. / Zhang, Q. / Hang, T. / Tao, Y. / Ma, X. / Wu, M. / Zhang, X. / Zang, J.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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: Rpl8 peptide
D: Rpl8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,92512
Polymers108,1784
Non-polymers7478
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-73 kcal/mol
Surface area38200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.500, 202.930, 85.680
Angle α, β, γ (deg.)90.00, 118.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-809-

HOH

21B-804-

HOH

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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: 52984.836 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 176-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NO66, C14orf169, MAPJD / Production host: Escherichia coli (E. coli)
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 Rpl8 peptide


Mass: 1104.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62917*PLUS

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Non-polymers , 5 types, 571 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 6.5, 0.5 M Sodium acetate trihydrate
PH range: 5.5 -7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 62029 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata processing
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementResolution: 2.2→40.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 5.743 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26154 3314 5.1 %RANDOM
Rwork0.20279 ---
obs0.20578 62029 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.25 Å2
2---0.05 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7480 0 44 563 8087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197744
X-RAY DIFFRACTIONr_bond_other_d0.0020.027241
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.96810531
X-RAY DIFFRACTIONr_angle_other_deg0.96316591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18422.883385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.194151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.021577
X-RAY DIFFRACTIONr_chiral_restr0.1130.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021880
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.032.3183780
X-RAY DIFFRACTIONr_mcbond_other2.032.3173778
X-RAY DIFFRACTIONr_mcangle_it3.0583.4644722
X-RAY DIFFRACTIONr_mcangle_other3.0573.4654723
X-RAY DIFFRACTIONr_scbond_it2.412.5063964
X-RAY DIFFRACTIONr_scbond_other2.412.5063965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6373.6685810
X-RAY DIFFRACTIONr_long_range_B_refined6.19719.1079461
X-RAY DIFFRACTIONr_long_range_B_other6.19619.1089462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 250 -
Rwork0.285 4600 -
obs--97.61 %

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