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- PDB-3pdq: Crystal structure of JMJD2A complexed with bipyridyl inhibitor -

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Basic information

Entry
Database: PDB / ID: 3pdq
TitleCrystal structure of JMJD2A complexed with bipyridyl inhibitor
ComponentsLysine-specific demethylase 4A
KeywordsOxidoreductase/Oxidoreductase inhibitor / jmjC Domain / Oxidoreductase / Chromatin Regulator / Dioxygenase / Transcription / Iron / 2-oxoglutarate / alpha-ketoglutarate / Demethylation / Nucleus / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol
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 ...: / : / : / 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. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-KC6 / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.989 Å
AuthorsKing, O.N.F. / Chang, K.-H. / Rose, N.R. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Chemmedchem / Year: 2011
Title: Inhibition of histone demethylases by 4-carboxy-2,2'-bipyridyl compounds
Authors: Chang, K.-H. / King, O.N.F. / Tumber, A. / Woon, E.C. / Heightman, T.D. / McDonough, M.A. / Schofield, C.J. / Rose, N.R.
History
DepositionOct 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 1, 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.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_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 4A
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,69715
Polymers88,6532
Non-polymers1,04413
Water9,944552
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9019
Polymers44,3261
Non-polymers5758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7956
Polymers44,3261
Non-polymers4695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.770, 149.440, 57.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: Catalytic domain, residues 1-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O75164, 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

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Non-polymers , 6 types, 565 molecules

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


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-KC6 / 4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid


Mass: 286.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N4O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.43 Å3/Da / Density % sol: 49.45 % / Mosaicity: 0.33 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Citrate, 4mM NiCl2, 17.5% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2010 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 6.3 % / Number: 379832 / Rmerge(I) obs: 0.087 / D res high: 1.99 Å / D res low: 53.5 Å
ReflectionResolution: 1.989→83.549 Å / Num. all: 60331 / Num. obs: 60331 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 27.67 Å2 / Rsym value: 0.087 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.99-2.16.30.6530.5991.35504986980.2570.6530.5993100
2.1-2.226.40.4030.372.15297882460.1580.4030.374.8100
2.22-2.386.40.2590.2383.24965877440.1020.2590.2387100
2.38-2.576.40.180.1654.64619172040.070.180.1659.4100
2.57-2.816.40.1320.1215.94265866950.0520.1320.12113.5100
2.81-3.146.30.0830.07693851960820.0330.0830.07618.3100
3.14-3.636.20.060.05511.53367653910.0240.060.05523.9100
3.63-4.456.10.080.0737.82806045880.0310.080.07328.5100
4.45-6.295.80.0530.04911.12089536080.0220.0530.0493199.9
6.29-49.8135.90.0310.02821.81214820750.0120.0310.02833.498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OX0

2ox0


Resolution: 1.989→45.469 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.27 / σ(F): 0.03 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2950 5.05 %Random
Rwork0.167 ---
all0.169 58409 --
obs0.169 58409 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.426 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 112.46 Å2 / Biso mean: 36.2503 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1--1.4143 Å20 Å20 Å2
2--0.1813 Å2-0 Å2
3---1.2331 Å2
Refinement stepCycle: LAST / Resolution: 1.989→45.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5651 0 53 552 6256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085989
X-RAY DIFFRACTIONf_angle_d1.0878148
X-RAY DIFFRACTIONf_chiral_restr0.076839
X-RAY DIFFRACTIONf_plane_restr0.0071052
X-RAY DIFFRACTIONf_dihedral_angle_d15.5092166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.989-2.02160.28351310.22822384251589
2.0216-2.05650.27291320.21462499263191
2.0565-2.09390.24551490.20612447259692
2.0939-2.13410.27941340.20182490262493
2.1341-2.17770.26661310.19822571270295
2.1777-2.2250.24431360.18452589272595
2.225-2.27680.23511380.17232570270896
2.2768-2.33370.21011310.16622585271697
2.3337-2.39680.21341570.16572636279397
2.3968-2.46740.2171260.16352637276397
2.4674-2.5470.20221370.16832648278598
2.547-2.6380.22591550.17292646280198
2.638-2.74360.21281460.17332695284199
2.7436-2.86850.22631540.17612686284099
2.8685-3.01970.24811300.18032698282899
3.0197-3.20880.19041370.17012731286899
3.2088-3.45650.21071450.163527102855100
3.4565-3.80420.1871410.154127572898100
3.8042-4.35430.16461400.137227702910100
4.3543-5.48440.1521600.124427812941100
5.4844-45.48120.17391400.15982929306999
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)
10.7892-0.64450.67431.6605-0.64151.68110.39620.4945-0.5857-0.3398-0.03831.24850.3889-0.6164-0.02170.38410.114-0.18030.4613-0.08510.4043-44.4841-28.2049-31.2909
21.055-0.970.65451.632-0.10340.70750.48230.7332-0.3158-0.4805-0.47890.33740.29090.1171-0.26230.33320.168-0.09870.4519-0.07240.1497-36.931-23.6296-34.7298
32.0512-0.33450.80412.309-0.51741.00630.29690.58380.0205-0.1662-0.4724-0.57940.13420.46390.24470.12990.13430.15190.37220.12480.1664-13.1935-25.2443-25.2406
41.9882-0.85840.68431.0944-0.29310.26720.21420.37190.1946-0.2163-0.2916-0.02290.03490.1745-0.00010.16840.05680.03750.2620.05110.1196-28.2309-17.7417-26.1745
50.05520.0459-0.08010.0246-0.07990.0979-0.0201-0.2905-0.2770.31020.04180.3735-0.0841-0.21960.00020.2745-0.00620.07480.17240.03150.2739-34.2279-32.0318-7.2934
60.3427-0.01120.03760.1865-0.06790.1778-0.1298-0.41540.16750.3313-0.1449-0.141-0.3499-0.0473-0.0030.2498-0.03550.00130.27390.0070.1498-25.8968-23.7536-3.6509
70.1347-0.02230.03460.05560.019-0.03640.0919-0.07950.0139-0.007-0.0928-0.17760.01970.0523-0.00010.1591-0.01510.03790.16430.04250.18-24.8813-33.653-12.18
81.4939-0.94430.66491.0019-0.70640.25690.17810.2153-0.0227-0.1501-0.20730.22810.07190.091700.15690.0178-0.00690.2049-0.02060.133-32.8697-22.7978-21.2049
90.6697-0.9576-0.44770.9089-0.15071.2109-0.0015-0.039-0.11390.1376-0.02620.3256-0.0859-0.26150.00010.07010.0275-0.00360.1173-0.03740.2228-47.9829-14.1732-13.6388
100.90140.081-0.23390.6805-0.45840.28890.07990.14940.3593-0.2891-0.0857-0.52710.18830.19450.00110.3030.01930.08720.1630.00480.2768-26.7508-52.1435-8.238
110.1079-0.00670.01941.4537-0.46780.3462-0.13880.40570.0602-0.35780.26190.42880.5226-0.70410.31770.5176-0.266-0.19690.3875-0.02440.1789-51.7276-64.4131-8.682
120.32370.0033-0.22960.0148-0.00620.1287-0.03440.01590.09390.14170.1070.29240.1749-0.077800.1856-0.0648-0.06280.26760.02760.2443-54.4898-50.873710.9058
130.8923-0.3126-0.74870.27430.47870.9374-0.06880.34210.1163-0.69590.24220.38580.1087-0.67510.07310.3425-0.1754-0.19880.51280.18340.2848-56.9181-49.9531-6.8152
140.9862-0.0138-0.19660.6116-0.12951.06750.00720.0051-0.0244-0.22210.1428-0.08620.3102-0.189700.2647-0.0586-0.08380.11270.0080.169-41.7182-57.9188-0.3936
150.1116-0.2679-0.09040.50660.15630.4092-0.1094-0.51510.09540.03120.0523-0.1622-0.09160.12950.00010.2062-0.0041-0.06720.2735-0.06120.2174-38.322-47.964118.6962
160.2736-0.0017-0.07920.068-0.07210.20510.1271-0.09890.0216-0.02520.20870.0614-0.1109-0.20690.00220.1939-0.04-0.03240.16310.00820.27-43.1698-40.887311.3147
170.9738-0.6081-0.27440.5803-0.32950.7233-0.0104-0.1208-0.02-0.14040.0706-0.11120.1074-0.040800.1805-0.0428-0.04520.0830.01390.1656-35.3913-54.2943.9668
180.0952-0.2870.07090.226-0.1460.38250.1186-0.2328-0.25310.02210.0298-0.0221-0.0584-0.02130.00020.26310.054-0.00270.22060.04320.3849-20.882-66.730615.9742
190.1275-0.150.05380.0499-0.02130.06270.0221-0.12090.09940.023-0.1673-0.6091-0.01920.4487-0.00010.21150.04460.02550.3117-0.01180.5538-17.5128-53.52773.6492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:29)A3 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:61)A30 - 61
3X-RAY DIFFRACTION3(chain A and resid 62:123)A62 - 123
4X-RAY DIFFRACTION4(chain A and resid 124:213)A124 - 213
5X-RAY DIFFRACTION5(chain A and resid 214:225)A214 - 225
6X-RAY DIFFRACTION6(chain A and resid 226:239)A226 - 239
7X-RAY DIFFRACTION7(chain A and resid 240:254)A240 - 254
8X-RAY DIFFRACTION8(chain A and resid 255:309)A255 - 309
9X-RAY DIFFRACTION9(chain A and resid 310:355)A310 - 355
10X-RAY DIFFRACTION10(chain B and resid 7:54)B7 - 54
11X-RAY DIFFRACTION11(chain B and resid 55:72)B55 - 72
12X-RAY DIFFRACTION12(chain B and resid 73:91)B73 - 91
13X-RAY DIFFRACTION13(chain B and resid 92:117)B92 - 117
14X-RAY DIFFRACTION14(chain B and resid 118:213)B118 - 213
15X-RAY DIFFRACTION15(chain B and resid 214:240)B214 - 240
16X-RAY DIFFRACTION16(chain B and resid 241:253)B241 - 253
17X-RAY DIFFRACTION17(chain B and resid 254:311)B254 - 311
18X-RAY DIFFRACTION18(chain B and resid 312:338)B312 - 338
19X-RAY DIFFRACTION19(chain B and resid 339:354)B339 - 354

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