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- PDB-3rvh: Crystal Structure of JMJD2A Complexed with Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3rvh
TitleCrystal Structure of JMJD2A Complexed with Inhibitor
ComponentsLysine-specific demethylase 4A
KeywordsOxidoreductase/Oxidoreductase Inhibitor / Oxidoreductase / jmjC Domain / 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 / 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 / response to nutrient levels / 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 / 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
Chem-HQ2 / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsKing, O.N.F. / Maloney, D.J. / Tumber, A. / Rai, G. / Jadhav, A. / Clifton, I.J. / Heightman, T.D. / Simeonov, A. / McDonough, M.A. / Schofield, C.J.
CitationJournal: To be Published
Title: Crystal Structure of JMJD2A Complexed with Inhibitor
Authors: King, O.N.F. / Maloney, D.J. / Tumber, A. / Rai, G. / Jadhav, A. / Clifton, I.J. / Heightman, T.D. / Simeonov, A. / McDonough, M.A. / Schofield, C.J.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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 4A
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,63210
Polymers88,6532
Non-polymers9798
Water6,413356
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8165
Polymers44,3261
Non-polymers4894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8165
Polymers44,3261
Non-polymers4894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.820, 149.340, 57.154
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JHDM3A, JMJD2, JMJD2A, KDM4A, KIAA0677 / 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 , 5 types, 364 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-HQ2 / 8-hydroxy-3-(piperazin-1-yl)quinoline-5-carboxylic acid


Mass: 273.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N3O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 49.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M CITRATE, 4mM NiCl2, 20% PEG 3350, 2:1 Protein:Well, 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: I04 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2010 / Details: mirrors
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 41678 / Num. obs: 41678 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.081 / Χ2: 0.887 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.294.40.62120300.738199
2.29-2.334.60.53620250.778199.6
2.33-2.384.60.49420780.773199.4
2.38-2.424.70.4320510.749199.5
2.42-2.484.70.39120340.796199.4
2.48-2.534.70.35120530.793199.8
2.53-2.64.70.30420780.788199.8
2.6-2.674.80.25920410.817199.8
2.67-2.754.70.20420420.87199.7
2.75-2.834.70.17920780.9199.9
2.83-2.944.80.1520610.935199.9
2.94-3.054.80.11420971.048199.8
3.05-3.194.80.08920771.079199.9
3.19-3.364.80.0820820.9891100
3.36-3.574.90.07520980.9511100
3.57-3.854.80.07121030.7771100
3.85-4.234.80.05820970.9881100
4.23-4.854.70.04721521.0571100
4.85-6.14.60.04121510.9561100
6.1-504.50.03422500.91198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OX0

2ox0


Resolution: 2.251→45.385 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.63 / σ(F): 1.35 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 2117 5.08 %RANDOM
Rwork0.1756 ---
obs0.1781 41635 99.68 %-
all-41635 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.788 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 144.08 Å2 / Biso mean: 44.0446 Å2 / Biso min: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.0506 Å20 Å20 Å2
2--0.7829 Å2-0 Å2
3---1.2677 Å2
Refinement stepCycle: LAST / Resolution: 2.251→45.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 56 356 6032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085955
X-RAY DIFFRACTIONf_angle_d1.0688115
X-RAY DIFFRACTIONf_chiral_restr0.073841
X-RAY DIFFRACTIONf_plane_restr0.0051043
X-RAY DIFFRACTIONf_dihedral_angle_d13.1432165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.251-2.3030.33141260.23892575270199
2.303-2.36060.26951380.221125892727100
2.3606-2.42450.27971350.219226092744100
2.4245-2.49580.31791310.210625962727100
2.4958-2.57630.27571620.215925962758100
2.5763-2.66840.27811290.201325902719100
2.6684-2.77520.25471530.196125882741100
2.7752-2.90150.26281240.200526272751100
2.9015-3.05450.24921540.18626332787100
3.0545-3.24580.2141530.170626112764100
3.2458-3.49630.24661310.180226602791100
3.4963-3.8480.19641340.170426622796100
3.848-4.40440.20931500.142626762826100
4.4044-5.54750.15651480.133926922840100
5.5475-45.39430.20421490.18132814296399
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)
10.0451-0.01820.00770.0077-0.00260.0016-0.2769-0.50410.38170.7902-0.16550.9376-0.0775-0.49820.05390.7906-0.2334-0.07410.69650.00580.8175-49.7519-35.3671-20.7297
21.3743-0.4539-0.01051.5882-0.2441.4060.34691.0895-0.0612-0.9111-0.5340.31170.20740.07560.01570.42430.1635-0.09140.4863-0.00610.1735-35.7068-22.6985-34.3159
31.53580.3872-0.05571.256-0.80391.3580.39020.6508-0.0845-0.2778-0.3681-0.45930.34340.60640.15790.23710.10760.19510.56230.12120.2276-13.1097-27.7652-24.2572
41.4907-0.67910.30951.54910.05340.54090.19780.35190.2033-0.3359-0.2816-0.0105-0.06410.2030.05920.23980.04580.0180.3250.05260.1917-28.4979-17.8213-26.3339
53.71310.1930.67883.5706-0.66653.3888-0.1138-0.5669-0.18770.51-0.24060.0058-0.09870.23690.35740.402-0.02350.07140.32830.00510.2769-29.6029-27.5712-5.6761
62.68691.7758-0.72374.03830.1122.3230.1058-0.0457-0.20530.0071-0.2195-0.5608-0.07620.11060.01420.2146-0.02410.05020.22050.02390.2587-24.9301-35.0402-12.3552
72.3412-1.10320.43422.0121-0.97891.05580.1940.1474-0.0937-0.2518-0.18690.24210.03820.1068-0.00020.19960.0032-0.03250.2448-0.03940.2012-33.5795-23.5018-22.0184
81.6724-1.0742-1.04692.667-0.13672.2250.0749-0.0698-0.20850.2253-0.00050.2406-0.2309-0.2909-0.04460.27770.0349-0.02820.3085-0.06470.4143-47.274-13.6944-13.1023
92.4819-0.42420.91751.0563-0.81830.78440.1207-0.3517-0.14670.3077-0.3231-0.8114-0.20960.585-0.08230.5366-0.29850.05581.089-0.25551.4866-18.9667-43.0180.9421
103.0702-0.2343-0.45742.2665-0.2551.70040.09850.44360.0147-0.72210.0604-0.57880.33290.1194-0.1340.4856-0.00990.04920.22610.00150.2298-31.2061-55.132-9.8124
110.9412-0.20290.161.19850.90511.1556-0.10870.00580.0018-0.13230.17740.48810.2267-0.51240.05350.3042-0.1984-0.13470.4260.04250.2796-56.3436-56.03663.0524
122.6616-0.67721.01820.65650.76942.5973-0.00290.1730.4421-0.40490.14640.3523-0.1477-0.34840.08580.2983-0.0203-0.12530.33710.14920.3238-54.3548-41.438-1.6102
131.6664-0.07670.00360.88380.11731.33070.0742-0.0464-0.2774-0.29510.1226-0.14730.5822-0.1476-0.13190.4271-0.0555-0.06580.1534-0.00040.2531-39.958-61.0017-0.834
143.37230.6838-1.17192.55450.10652.79650.0793-0.9890.20450.4976-0.1828-0.104-0.25720.07320.20570.3379-0.0248-0.08070.4355-0.04820.3817-38.1357-48.004417.9859
150.9977-0.4756-0.34071.4498-0.15951.39090.0138-0.01840.0837-0.0820.1211-0.22540.1144-0.03-0.08520.2221-0.0541-0.02510.14550.0030.2523-38.9727-48.76082.277
161.8665-0.99651.07122.7822-0.58391.8595-0.0649-0.16970.02470.0506-0.0338-0.09070.1259-0.0266-0.00130.28670.0464-0.02580.28590.01380.4133-22.8558-61.561212.996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:11)A3 - 11
2X-RAY DIFFRACTION2(CHAIN A AND RESID 12:70)A12 - 70
3X-RAY DIFFRACTION3(CHAIN A AND RESID 71:123)A71 - 123
4X-RAY DIFFRACTION4(CHAIN A AND RESID 124:213)A124 - 213
5X-RAY DIFFRACTION5(CHAIN A AND RESID 214:240)A214 - 240
6X-RAY DIFFRACTION6(CHAIN A AND RESID 241:254)A241 - 254
7X-RAY DIFFRACTION7(CHAIN A AND RESID 255:307)A255 - 307
8X-RAY DIFFRACTION8(CHAIN A AND RESID 308:353)A308 - 353
9X-RAY DIFFRACTION9(CHAIN B AND RESID 5:9)B5 - 9
10X-RAY DIFFRACTION10(CHAIN B AND RESID 10:64)B10 - 64
11X-RAY DIFFRACTION11(CHAIN B AND RESID 65:103)B65 - 103
12X-RAY DIFFRACTION12(CHAIN B AND RESID 104:128)B104 - 128
13X-RAY DIFFRACTION13(CHAIN B AND RESID 129:211)B129 - 211
14X-RAY DIFFRACTION14(CHAIN B AND RESID 212:241)B212 - 241
15X-RAY DIFFRACTION15(CHAIN B AND RESID 242:294)B242 - 294
16X-RAY DIFFRACTION16(CHAIN B AND RESID 295:354)B295 - 354

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