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- PDB-2xml: Crystal structure of human JMJD2C catalytic domain -

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Basic information

Entry
Database: PDB / ID: 2xml
TitleCrystal structure of human JMJD2C catalytic domain
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4CKDM4C
KeywordsOXIDOREDUCTASE / TRANSCRIPTION REGULATION / METAL BINDING
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
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsYue, W.W. / Gileadi, C. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Ng, S. / Carpenter, L. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Yue, W.W. / Gileadi, C. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Ng, S. / Carpenter, L. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human Kdm4 Histone Demethylase Family.
Authors: Hillringhaus, L. / Yue, W.W. / Rose, N.R. / Ng, S.S. / Gileadi, C. / Loenarz, C. / Bello, S.H. / Bray, J.E. / Schofield, C.J. / Oppermann, U.
History
DepositionJul 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: 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)81,69412
Polymers80,9302
Non-polymers76410
Water5,170287
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A: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9588
Polymers40,4651
Non-polymers4937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7364
Polymers40,4651
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.660, 95.870, 100.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 10:161 OR RESSEQ 174:313 OR RESSEQ 315:347 )
211CHAIN B AND (RESSEQ 10:161 OR RESSEQ 174:313 OR RESSEQ 315:347 )

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40465.168 Da / Num. of mol.: 2 / Fragment: JUMONJI DOMAIN, RESIDUES 1-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
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, 297 molecules

#2: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.55 Å3/Da / Density % sol: 51.74 % / Description: NONE
Crystal growDetails: 0.2M NA_NITRATE; 15% PEG_3350; 5% V/V ETHYLENE_GLYCOL; 0.1M BIS_TRIS_PROPANE PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: MARRESEARCH / Detector: CCD / Date: May 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.55→88.66 Å / Num. obs: 28447 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 20.41 Å2 / Rmerge(I) obs: 0.37 / Net I/σ(I): 7.3
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.4 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQ7

2oq7


Resolution: 2.55→40.572 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1388 5 %
Rwork0.1961 --
obs0.1991 27764 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.849 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3933 Å20 Å20 Å2
2--0.4056 Å20 Å2
3----0.1553 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5471 0 37 287 5795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085698
X-RAY DIFFRACTIONf_angle_d1.2027721
X-RAY DIFFRACTIONf_dihedral_angle_d13.7972086
X-RAY DIFFRACTIONf_chiral_restr0.077792
X-RAY DIFFRACTIONf_plane_restr0.004991
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2645X-RAY DIFFRACTIONPOSITIONAL
12B2645X-RAY DIFFRACTIONPOSITIONAL0.099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.64110.34751360.25662506X-RAY DIFFRACTION94
2.6411-2.74690.29091250.23372636X-RAY DIFFRACTION98
2.7469-2.87190.29661450.22252606X-RAY DIFFRACTION98
2.8719-3.02320.29751420.22072599X-RAY DIFFRACTION97
3.0232-3.21260.2841370.20062662X-RAY DIFFRACTION99
3.2126-3.46050.2471460.19192662X-RAY DIFFRACTION99
3.4605-3.80850.23621260.16982621X-RAY DIFFRACTION96
3.8085-4.3590.21871530.15552681X-RAY DIFFRACTION98
4.359-5.48980.19521310.14562660X-RAY DIFFRACTION96
5.4898-40.57710.20191470.18522743X-RAY DIFFRACTION95
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)
10.39320.0102-0.09090.5567-0.16210.36110.03530.11230.0950.00980.01330.0637-0.0184-0.1143-0.34960.02470.06470.01110.05620.04850.023846.756226.669547.016
20.7654-0.23470.0820.0719-0.02510.0090.16660.23340.08430.008-0.13820.049-0.013-0.0145-0.59480.08180.05870.04940.1201-0.02770.033760.932627.387934.6853
30.63840.29110.24670.209-0.01550.42840.1027-0.0269-0.06140.0695-0.0051-0.0384-0.1144-0.12940.01390.06190.06990.02110.03790.00150.065449.335627.581151.7859
41.97070.37330.24490.74560.11380.03730.0609-0.2758-0.0013-0.1192-0.1035-0.1515-0.0272-0.0646-0.03080.04780.02150.00010.03940.01160.089559.217710.717255.3309
50.5825-0.11090.04410.1781-0.01620.2918-0.0294-0.0933-0.05070.11650.02060.0208-0.0085-0.1737-0.01610.03520.0283-0.00840.08270.0120.023144.282119.011962.5539
61.3442-0.44590.7330.3334-0.48480.9107-0.00670.0255-0.0419-0.0393-0.0352-0.0152-0.01670.1016-0.00780.04130.05810.01150.0101-0.00290.00415.135121.583962.9305
70.3831-0.18120.48520.1948-0.06440.944-0.02350.09290.2204-0.0182-0.0212-0.1606-0.00650.17090.00990.0824-0.0092-0.01970.02820.03470.166415.978936.932955.8633
80.3844-0.12410.10420.1908-0.05670.4507-0.0456-0.0149-0.07650.00360.0352-0.0583-0.03440.0407-0.04720.06750.04430.01310.0369-0.00080.07671.272626.842251.5122
90.8583-0.33660.69970.40220.48163.9118-0.01130.25720.0937-0.0546-0.2411-0.0493-0.39540.0506-0.27160.0686-0.01690.02780.11580.05420.0623-5.136737.718334.1264
100.0263-0.00140.00830.00130.00790.0589-0.0953-0.0428-0.02810.15910.05180.1461-0.0341-0.0346-0.00930.28510.20920.00160.146-0.06750.2067-4.456441.425551.5718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 10:99)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 100:120)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 121:215)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 216:262)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 263:347)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 10:220)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 221:262)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 263:329)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 330:342)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 343:347)

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