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- PDB-4gd4: Crystal Structure of JMJD2A Complexed with Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4gd4
TitleCrystal Structure of JMJD2A Complexed with Inhibitor
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Structural Genomics / Structural Genomics Consortium / SGC / OXIDOREDUCTASE / JMJC DOMAIN / CHROMATIN REGULATOR / DIOXYGENASE / TRANSCRIPTION / DEMETHYLATION / IRON / 2-OXOGLUTARATE / ALPHA-KETOGLUTARATE / NUCLEUS / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / 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 / positive regulation of gene expression / 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-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsKing, O.N.F. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / McDonough, M.A. / Schofield, C.J. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of JMJD2A Complexed with Inhibitor
Authors: King, O.N.F. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / McDonough, M.A. / Schofield, C.J. / Structural Genomics Consortium (SGC)
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Dec 3, 2014Group: Structure summary
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 28, 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 / 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
Remark 0 : statistics at the very beginning when nothing is done yet

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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)89,42112
Polymers88,6532
Non-polymers76810
Water5,837324
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6755
Polymers44,3261
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7467
Polymers44,3261
Non-polymers4206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.750, 150.030, 57.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Production host: Escherichia coli (E. coli)
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 , 5 types, 334 molecules

#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-0WS / 2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid


Mass: 189.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7N3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M NaF, 20% w/v PEG 3350, 0.1 M Bis Tris Propane, pH 7.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.33→83.64 Å / Num. all: 37798 / Num. obs: 37798 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 50.59 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2766 / % possible all: 99.9

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→83.64 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9342 / SU R Cruickshank DPI: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 1882 4.99 %RANDOM
Rwork0.1801 ---
all0.182 37741 --
obs0.182 37741 99.1 %-
Displacement parametersBiso mean: 50.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.6443 Å20 Å20 Å2
2--2.097 Å20 Å2
3----2.7413 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.33→83.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 36 324 5955
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015862HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037982HARMONIC2
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes912HARMONIC5
X-RAY DIFFRACTIONt_it5862HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion2.82
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2992 128 4.65 %
Rwork0.2273 2623 -
all0.2305 2751 -
obs--99.1 %
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)
10.03211.64251.20690-0.00060.4541-0.00660.023-0.04690.0340.09760.16830.0056-0.1941-0.09090.0858-0.0823-0.2034-0.128-0.0220.0807-46.1042-36.3714-22.0915
23.3713-1.10020.9383.0614-0.91011.45620.44570.9140.1189-0.7637-0.6428-0.14030.25230.41890.1971-0.0690.18740.09660.07260.0596-0.2755-26.1045-21.7433-28.3807
34.47791.24840.24667.1441-0.97521.64140.1057-0.3249-0.0980.3636-0.28940.0860.0288-0.0120.1836-0.0724-0.04120.0672-0.0602-0.0171-0.0959-29.4715-27.4709-7.8589
42.7225-1.81121.07362.929-1.20641.37030.33890.3795-0.1454-0.43-0.42270.16870.1910.1640.0838-0.01210.02250.01840.0369-0.0215-0.0211-31.686-25.2733-19.6849
52.603-0.3954-2.33641.6218-2.14363.44510.0503-0.21360.2950.35090.0450.4066-0.2736-0.3053-0.0954-0.13530.06840.0347-0.1102-0.08340.0377-47.5018-8.6014-11.4092
60.4637-3.5152-2.68053.64270.35032.36090.123-0.0243-0.24180.2566-0.00430.55810.129-0.2463-0.1188-0.224-0.03780.0186-0.0495-0.0160.1835-50.8886-22.0218-16.7157
70.05410.7034-0.74930.21440.9130.4632-0.00670.03090.0207-0.04660.0092-0.05910.02590.0853-0.0025-0.1641-0.2107-0.06350.0191-0.13240.2178-24.5429-40.9055-0.1088
82.80050.4079-0.53382.7457-0.6752.4609-0.05980.4270.0143-0.85080.25750.0520.7484-0.3918-0.19770.1301-0.1752-0.1725-0.17920.0575-0.2693-42.7574-55.8237-4.7094
92.24720.08810.13882.501-0.93422.62870.01060.0195-0.0222-0.45210.22940.01460.4411-0.2561-0.24-0.0385-0.1084-0.115-0.16830.0259-0.1315-41.8105-54.50553.2755
101.1992-0.3843-0.0732.3141-1.15612.26870.0157-0.06320.0256-0.29170.1412-0.16370.326-0.0847-0.157-0.0188-0.0826-0.0614-0.0972-0.015-0.0141-36.234-51.77874.7656
112.101-3.86825.12394.6862-1.92944.7943-0.009-0.4916-0.1552-0.18360.1464-0.3278-0.00110.0036-0.1374-0.02290.0280.0319-0.07510.04160.0633-21.2801-67.246416.0423
123.4586-2.62771.97680.01480.315500.06080.0433-0.0003-0.1017-0.2076-0.35650.11890.3620.1468-0.14550.041-0.0155-0.0882-0.03020.1899-17.5692-53.86483.7186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|13 }A5 - 13
2X-RAY DIFFRACTION2{ A|14 - A|209 }A14 - 209
3X-RAY DIFFRACTION3{ A|210 - A|243 }A210 - 243
4X-RAY DIFFRACTION4{ A|244 - A|311 }A244 - 311
5X-RAY DIFFRACTION5{ A|312 - A|333 }A312 - 333
6X-RAY DIFFRACTION6{ A|334 - A|354 }A334 - 354
7X-RAY DIFFRACTION7{ B|8 - B|13 }B8 - 13
8X-RAY DIFFRACTION8{ B|14 - B|107 }B14 - 107
9X-RAY DIFFRACTION9{ B|108 - B|245 }B108 - 245
10X-RAY DIFFRACTION10{ B|246 - B|310 }B246 - 310
11X-RAY DIFFRACTION11{ B|311 - B|338 }B311 - 338
12X-RAY DIFFRACTION12{ B|339 - B|354 }B339 - 354

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