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- PDB-5fjh: Crystal structure of human JMJD2C catalytic domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5fjh
TitleCrystal structure of human JMJD2C catalytic domain in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino) -2-oxoethyl)amino)methyl)isonicotinic acid
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4CKDM4C
KeywordsOXIDOREDUCTASE / TRANSCRIPTION REGULATION / METAL BINDING / DEMETHYLASE / LYSINE-SPECIFIC DEMETHYLASE 4C
Function / homology
Function and homology information


H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway ...H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / nuclear receptor coactivator activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / regulation of gene expression / chromatin remodeling / positive regulation of cell population proliferation / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / 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. / Small domain found in the jumonji family of transcription factors ...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-MMK / NICKEL (II) ION / Lysine-specific demethylase 4C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCecatiello, V. / Pasqualato, S.
CitationJournal: To be Published
Title: Crystal Structures of Human Jmjd2C Catalytic Domain Bound to Inhibitors
Authors: Cecatiello, V. / Pasqualato, S.
History
DepositionOct 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_conn.ptnr2_label_seq_id / _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 4C
B: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,02811
Polymers81,0342
Non-polymers9949
Water9,584532
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A: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0456
Polymers40,5171
Non-polymers5285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9835
Polymers40,5171
Non-polymers4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 95.920, 100.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-2185-

HOH

21B-2186-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.001466, 0.000877), (0.00147, 1, -0.004303), (-0.00087, 0.004305, 1)
Vector: 44.58, 48.36, -10.19)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 4C / KDM4C / JMJD2C / GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN / GASC-1 PROTEIN / JMJC DOMAIN- ...JMJD2C / GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN / GASC-1 PROTEIN / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3C / JUMONJI DOMAIN-CONTAINING PROTEIN 2C


Mass: 40517.246 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 3-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9H3R0, 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, 541 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-MMK / 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid


Mass: 306.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N4O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 7.25
Details: 21% PEG 3350 5% 1,2-ETHANEDIOL 0.2 M NANO3 0.1 M BIS-TRIS PROPANE PH 7.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→54.77 Å / Num. obs: 50575 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XML

2xml


Resolution: 2.1→54.767 Å / SU ML: 0.23 / σ(F): 1.99 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 2475 4.9 %
Rwork0.1847 --
obs0.1867 50483 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→54.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5496 0 54 532 6082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085707
X-RAY DIFFRACTIONf_angle_d0.957725
X-RAY DIFFRACTIONf_dihedral_angle_d15.0793352
X-RAY DIFFRACTIONf_chiral_restr0.056788
X-RAY DIFFRACTIONf_plane_restr0.006987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.14050.28931300.28542668X-RAY DIFFRACTION99
2.1405-2.18420.31361230.26792634X-RAY DIFFRACTION99
2.1842-2.23170.29621130.25342661X-RAY DIFFRACTION98
2.2317-2.28360.26621220.23772643X-RAY DIFFRACTION99
2.2836-2.34070.27991320.22712642X-RAY DIFFRACTION99
2.3407-2.4040.29171390.2292639X-RAY DIFFRACTION99
2.404-2.47480.27971460.21042635X-RAY DIFFRACTION99
2.4748-2.55460.31251300.21572655X-RAY DIFFRACTION99
2.5546-2.64590.26321290.20972671X-RAY DIFFRACTION100
2.6459-2.75190.23481230.19662685X-RAY DIFFRACTION100
2.7519-2.87710.26051460.20432633X-RAY DIFFRACTION99
2.8771-3.02880.2511570.19692629X-RAY DIFFRACTION99
3.0288-3.21850.26281460.18912669X-RAY DIFFRACTION99
3.2185-3.4670.20621760.16042652X-RAY DIFFRACTION99
3.467-3.81580.19861200.14782698X-RAY DIFFRACTION99
3.8158-4.36780.15321770.14122682X-RAY DIFFRACTION99
4.3678-5.50210.15081450.13182701X-RAY DIFFRACTION98
5.5021-54.78520.21461210.1642811X-RAY DIFFRACTION96
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)
17.0505-3.2379-0.28384.9452-0.21662.5521-0.23010.3038-0.3735-0.02090.07520.51620.3706-0.42880.10530.2189-0.15680.00090.3323-0.04980.209179.7374113.1779134.4859
22.02820.3861-0.43280.8897-0.2620.96230.01540.04540.1253-0.009-0.0094-0.0542-0.10870.01020.01570.2291-0.0758-0.01130.22670.0270.154197.3532125.1941135.4099
32.3040.2745-0.7110.826-0.31571.1290.00220.04390.11360.0145-0.04080.0712-0.0717-0.05310.01150.2163-0.075-0.02340.2328-0.0050.185493.8912124.1405139.7836
42.16940.2119-0.22661.1178-0.26231.0597-0.0508-0.1132-0.1165-0.008-0.0166-0.08820.08920.04350.08030.1789-0.07680.02060.19180.01350.157997.6989115.4766142.4688
52.5701-0.7303-1.28872.1941-1.33214.4268-0.1628-0.21220.10160.189-0.0376-0.1892-0.0420.19460.16230.2343-0.0497-0.00250.34130.01110.184287.0714111.3467160.832
66.185-2.25150.63176.9134-0.16148.48580.0864-0.0899-0.54730.38230.32470.58390.5918-0.4312-0.26050.1909-0.01110.01210.3597-0.00520.257635.129665.4578144.4259
72.31020.659-0.52370.5843-0.41741.34740.01090.07710.23490.03530.04380.0593-0.1462-0.0894-0.03780.22880.0989-0.00480.1414-0.0140.158852.781777.3804145.2917
81.90110.1808-0.29220.7469-0.47191.64180.0376-0.17680.01580.04490.01750.0071-0.0854-0.0921-0.03690.20440.0667-0.00140.1527-0.02230.168752.073870.1391151.6249
97.8853-1.6803-2.16253.621-1.14116.9451-0.2701-0.187-0.0617-0.07510.1327-0.19440.36480.0780.08610.24030.08730.00430.29060.01950.158342.464863.5086170.6653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 28 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 29 THROUGH 115 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 116 THROUGH 166 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 167 THROUGH 295 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 296 THROUGH 347 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 10 THROUGH 28 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 29 THROUGH 115 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 116 THROUGH 295 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 296 THROUGH 347 )

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