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- PDB-2xdp: Crystal structure of the tudor domain of human JMJD2C -

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Basic information

Entry
Database: PDB / ID: 2xdp
TitleCrystal structure of the tudor domain of human JMJD2C
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4CKDM4C
KeywordsOXIDOREDUCTASE / HISTONE MODIFICATION
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 / chromatin / positive regulation of cell population proliferation / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...Vcp-like ATPase; Chain A, domain 2 - #70 / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / 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. / 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 / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 4C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYue, W.W. / Gileadi, C. / Krojer, T. / Weisbach, H. / Ugochukwu, E. / Daniel, M. / Phillips, C. / Chaikuad, A. / von Delft, F. / Allerston, C. ...Yue, W.W. / Gileadi, C. / Krojer, T. / Weisbach, H. / Ugochukwu, E. / Daniel, M. / Phillips, C. / Chaikuad, A. / von Delft, F. / Allerston, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Tudor Domain of Human Jmjd2C
Authors: Yue, W.W. / Gileadi, C. / Krojer, T. / Weisbach, H. / Ugochukwu, E. / Daniel, M. / Phillips, C. / Chaikuad, A. / von Delft, F. / Allerston, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / ...Authors: Yue, W.W. / Gileadi, C. / Krojer, T. / Weisbach, H. / Ugochukwu, E. / Daniel, M. / Phillips, C. / Chaikuad, A. / von Delft, F. / Allerston, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionMay 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Other ...Database references / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2492
Polymers14,1531
Non-polymers961
Water3,351186
1
A: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules

A: LYSINE-SPECIFIC DEMETHYLASE 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4984
Polymers28,3062
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area5500 Å2
ΔGint-58.6 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.815, 79.646, 81.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

21A-2064-

HOH

31A-2124-

HOH

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Components

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


Mass: 14153.049 Da / Num. of mol.: 1 / Fragment: TUDOR DOMAIN, RESIDUES 875-995
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
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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.04 Å3/Da / Density % sol: 59.51 % / Description: NONE
Crystal growDetails: 0.2M (NH4)2SO4; 0.1M TRIS PH 8.5; 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 20, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.56→18.58 Å / Num. obs: 24650 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / % possible all: 94.9

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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 2GFA

2gfa


Resolution: 1.56→18.512 Å / SU ML: 0.17 / σ(F): 1.15 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 2355 5.1 %
Rwork0.1857 --
obs0.1868 46098 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.375 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3042 Å20 Å2-0 Å2
2--10.274 Å20 Å2
3----0.9698 Å2
Refinement stepCycle: LAST / Resolution: 1.56→18.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 5 186 1138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009993
X-RAY DIFFRACTIONf_angle_d1.241346
X-RAY DIFFRACTIONf_dihedral_angle_d12.253375
X-RAY DIFFRACTIONf_chiral_restr0.1145
X-RAY DIFFRACTIONf_plane_restr0.006172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5601-1.59190.31971050.35642065X-RAY DIFFRACTION78
1.5919-1.62650.36321200.30642331X-RAY DIFFRACTION87
1.6265-1.66430.23711360.26722585X-RAY DIFFRACTION99
1.6643-1.70590.32251360.23542692X-RAY DIFFRACTION100
1.7059-1.7520.2211480.22192602X-RAY DIFFRACTION100
1.752-1.80350.21761380.19852638X-RAY DIFFRACTION99
1.8035-1.86170.2311390.19682624X-RAY DIFFRACTION100
1.8617-1.92820.21251420.17912602X-RAY DIFFRACTION100
1.9282-2.00530.19461330.17182650X-RAY DIFFRACTION100
2.0053-2.09640.2071550.17822670X-RAY DIFFRACTION100
2.0964-2.20680.20091360.17092592X-RAY DIFFRACTION99
2.2068-2.34480.2121370.17292624X-RAY DIFFRACTION99
2.3448-2.52540.20361470.17712655X-RAY DIFFRACTION99
2.5254-2.77880.18291130.17542643X-RAY DIFFRACTION100
2.7788-3.17910.19771800.17552578X-RAY DIFFRACTION99
3.1791-3.99870.17331530.16682597X-RAY DIFFRACTION99
3.9987-18.51280.1791370.16722595X-RAY DIFFRACTION98
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)
10.2473-0.0286-0.37881.95090.64232.04240.0341-0.65020.3044-0.04650.04670.2943-0.1443-0.2442-0.01680.14030.03780.00380.28460.00920.166344.830922.2944-1.9359
21.8892-0.32970.65581.0117-0.43481.04420.01960.7649-0.1019-0.0084-0.0527-0.23120.02110.38110.01630.0992-0.0061-0.0050.3574-0.06520.146712.973517.01042.0051
31.5986-0.4835-0.1330.55750.62650.8229-0.05610.12170.3571-0.22050.0653-0.0299-0.08370.0208-0.0080.2281-0.03610.0030.14250.03890.221723.249928.813519.6942
42.1667-0.1648-0.10690.110.34180.7112-0.01130.51410.3886-0.1873-0.0289-0.1233-0.09370.13950.08990.2505-0.04020.00830.20380.03520.271827.527327.929617.6071
50.84250.2430.33471.97230.0841.2458-0.07820.0982-0.20640.07280.1139-0.39750.01030.4297-0.10370.1697-0.0215-0.00280.2543-0.04680.220310.658217.98537.5417
60.49680.456-0.88960.7917-0.15312.47170.265-0.38650.1637-0.0546-0.1282-0.1283-0.02010.7786-0.06390.1748-0.01730.04360.4111-0.03340.206514.665625.3287-4.95
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 877:889)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 890:903)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 904:939)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 940:962)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 963:982)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 983:993)

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