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- PDB-4lxl: Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxy... -

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Basic information

Entry
Database: PDB / ID: 4lxl
TitleCrystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3
Components
  • H3 peptide
  • Lysine-specific demethylase 4B
KeywordsOXIDOREDUCTASE/PEPTIDE / JmjC domain / Demethylation / Histone / Methylation / Nucleus / OXIDOREDUCTASE-PEPTIDE complex
Function / homology
Function and homology information


histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling ...histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / brain development / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
Similarity search - Function
: / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. ...: / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / PYRIDINE-2,4-DICARBOXYLIC ACID / Lysine-specific demethylase 4B / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
human (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsWang, W.-C. / Chu, C.-H. / Chen, C.-C.
CitationJournal: To be Published
Title: Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3
Authors: Wang, W.-C. / Chu, C.-H. / Chen, C.-C.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Lysine-specific demethylase 4B
D: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5595
Polymers43,2682
Non-polymers2913
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-10 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.364, 78.475, 83.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein Lysine-specific demethylase 4B / JmjC domain-containing histone demethylation protein 3B / Jumonji domain-containing protein 2B


Mass: 42419.105 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP RESIDUES 1-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4B / Production host: Escherichia coli (E. coli)
References: UniProt: O94953, 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
#2: Protein/peptide H3 peptide


Mass: 849.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) human (human) / References: UniProt: P68431*PLUS

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Non-polymers , 4 types, 265 molecules

#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID / Lutidinic acid


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG8000, 0.2M magnesium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 22, 2013
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. all: 30463 / Num. obs: 30173 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.368 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YBS

2ybs


Resolution: 1.87→28.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.905 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1529 5.1 %RANDOM
Rwork0.1765 ---
obs0.1789 28644 --
all-30173 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.17 Å2 / Biso mean: 26.5967 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0 Å2
2---1.47 Å2-0 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.87→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 14 262 3025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192839
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9483841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.225335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02923.382136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35215478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0931518
X-RAY DIFFRACTIONr_chiral_restr0.1230.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212187
X-RAY DIFFRACTIONr_mcbond_it3.6033.1711346
X-RAY DIFFRACTIONr_mcangle_it4.7235.3091679
X-RAY DIFFRACTIONr_scbond_it5.123.6081493
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 114 -
Rwork0.225 2044 -
all-2158 -
obs--98.31 %

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