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- PDB-4hoo: Crystal structure of human JMJD2D/KDM4D apoenzyme -

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Basic information

Entry
Database: PDB / ID: 4hoo
TitleCrystal structure of human JMJD2D/KDM4D apoenzyme
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / Jumonji C demethylase / JMJD2/KDM4 family / beta barrel fold
Function / homology
Function and homology information


positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsKrishnan, S. / Trievel, R.C.
CitationJournal: Structure / Year: 2013
Title: Structural and Functional Analysis of JMJD2D Reveals Molecular Basis for Site-Specific Demethylation among JMJD2 Demethylases.
Authors: Krishnan, S. / Trievel, R.C.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,4088
Polymers76,0422
Non-polymers3666
Water2,756153
1
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2635
Polymers38,0211
Non-polymers2424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1453
Polymers38,0211
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.119, 73.119, 136.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 38020.961 Da / Num. of mol.: 2 / Fragment: UNP Residues 12-341 / Mutation: K93A, K94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM3D, JMJD2D, KDM4D / Plasmid: pHT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta 2)
References: UniProt: Q6B0I6, 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: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M calcium acetate, 0.1M HEPES pH 7.5, 10% PEG 8000, vapor diffusion, hanging drop, temperature 277.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.495→18 Å / Num. obs: 25850 / % possible obs: 91.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.078 / Χ2: 1.124 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.495-2.573.10.51420381.053187
2.57-2.664.10.44521401.076191.6
2.66-2.754.90.33722181.107194
2.75-2.865.30.2922881.154196.6
2.86-2.995.40.20822941.133198.4
2.99-3.155.60.14723371.202199.6
3.15-3.345.90.11724021.1961100
3.34-3.64.90.121681.217193.3
3.6-3.965.30.0819551.102140.2
3.96-4.5260.05822860.99197.9
4.52-5.676.10.04623671.093199.7
5.67-186.30.03723571.1151100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HON

4hon


Resolution: 2.495→17.93 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 24.455 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.709 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1311 5.1 %RANDOM
Rwork0.2071 ---
obs0.2092 25819 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.51 Å2 / Biso mean: 38.993 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-5.74 Å22.87 Å20 Å2
2--5.74 Å20 Å2
3----8.61 Å2
Refinement stepCycle: LAST / Resolution: 2.495→17.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5173 0 12 153 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215353
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9267287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1445660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43423.529255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54315796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6831527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214219
X-RAY DIFFRACTIONr_mcbond_it0.5491.53284
X-RAY DIFFRACTIONr_mcangle_it0.98825244
X-RAY DIFFRACTIONr_scbond_it1.23532069
X-RAY DIFFRACTIONr_scangle_it1.9694.52040
LS refinement shellResolution: 2.495→2.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 88 -
Rwork0.325 1649 -
all-1737 -
obs--85.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.02330.0704-0.68221.9639-0.18261.4785-0.08930.176-0.0431-0.14210.0616-0.0127-0.0637-0.09590.02780.0203-0.0053-0.02220.014-0.01190.7665-9.8287.1350.601
22.4934-0.6635-0.38462.47480.25541.1388-0.0208-0.1655-0.04580.1541-0.00640.0353-0.02220.10030.02710.0113-0.0047-0.01460.0180.0150.7483-25.34716.33549.106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 341
2X-RAY DIFFRACTION2B12 - 341

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