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- PDB-5ykn: crystal structure of Arabidopsis thaliana JMJ14 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 5ykn
Titlecrystal structure of Arabidopsis thaliana JMJ14 catalytic domain
ComponentsProbable lysine-specific demethylase JMJ14
KeywordsGENE REGULATION / JMJ14 / jumonji domain / C5HC2 zinc finger / H3K4me3 demethylase
Function / homology
Function and homology information


regulation of post-transcriptional gene silencing / : / L-pipecolic acid biosynthetic process / : / : / positive regulation of systemic acquired resistance / plant organ development / negative regulation of long-day photoperiodism, flowering / regulation of root development / negative regulation of flower development ...regulation of post-transcriptional gene silencing / : / L-pipecolic acid biosynthetic process / : / : / positive regulation of systemic acquired resistance / plant organ development / negative regulation of long-day photoperiodism, flowering / regulation of root development / negative regulation of flower development / regulation of root meristem growth / photoperiodism, flowering / plant-type hypersensitive response / positive regulation of defense response to bacterium / flower development / [histone H3]-trimethyl-L-lysine4 demethylase / : / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / negative regulation of gene expression, epigenetic / histone methyltransferase activity / developmental growth / histone demethylase activity / circadian rhythm / transcription cis-regulatory region binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
FY-rich, N-terminal / F/Y-rich N-terminus / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / Zinc finger, C5HC2-type / C5HC2 zinc finger ...FY-rich, N-terminal / F/Y-rich N-terminus / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / Zinc finger, C5HC2-type / C5HC2 zinc finger / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile.
Similarity search - Domain/homology
NICKEL (II) ION / Lysine-specific demethylase JMJ14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, Z. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0503200 China
CitationJournal: Plant Cell / Year: 2018
Title: Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases.
Authors: Yang, Z. / Qiu, Q. / Chen, W. / Jia, B. / Chen, X. / Hu, H. / He, K. / Deng, X. / Li, S. / Tao, W.A. / Cao, X. / Du, J.
History
DepositionOct 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable lysine-specific demethylase JMJ14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1914
Polymers65,0021
Non-polymers1903
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.143, 69.221, 100.414
Angle α, β, γ (deg.)90.00, 104.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable lysine-specific demethylase JMJ14 / Jumonji domain-containing protein 14 / Jumonji domain-containing protein 4 / Lysine-specific ...Jumonji domain-containing protein 14 / Jumonji domain-containing protein 4 / Lysine-specific histone demethylase JMJ14 / Protein JUMONJI 14


Mass: 65001.832 Da / Num. of mol.: 1 / Mutation: E180A, E181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JMJ14, JMJ4, PKDM7B, At4g20400, F9F13.50 / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q8GUI6, 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Na2SO4, 20% PEG 3350, 0.1M bis-tris propane, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 30445 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2967 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGQ

4igq


Resolution: 2.3→49.567 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.2217 1621 5.39 %
Rwork0.1942 --
obs0.1957 28454 99.04 %
all-30445 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3885 0 3 134 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063995
X-RAY DIFFRACTIONf_angle_d0.8515409
X-RAY DIFFRACTIONf_dihedral_angle_d15.8831475
X-RAY DIFFRACTIONf_chiral_restr0.051561
X-RAY DIFFRACTIONf_plane_restr0.005695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33430.30921070.3172372X-RAY DIFFRACTION97
2.3343-2.37080.41081060.33072429X-RAY DIFFRACTION99
2.3708-2.40970.39511450.31692410X-RAY DIFFRACTION99
2.4097-2.45120.29791560.30192416X-RAY DIFFRACTION99
2.4512-2.49580.34831420.2872386X-RAY DIFFRACTION100
2.4958-2.54380.35861470.28992499X-RAY DIFFRACTION100
2.5438-2.59570.35421230.2832427X-RAY DIFFRACTION100
2.5957-2.65220.27811740.25312367X-RAY DIFFRACTION100
2.6522-2.71390.28391560.25582438X-RAY DIFFRACTION100
2.7139-2.78170.33271080.24862479X-RAY DIFFRACTION100
2.7817-2.85690.30991570.24962398X-RAY DIFFRACTION100
2.8569-2.9410.26521370.23442417X-RAY DIFFRACTION100
2.941-3.03590.23551570.21992417X-RAY DIFFRACTION100
3.0359-3.14440.27631110.21872476X-RAY DIFFRACTION100
3.1444-3.27030.24151320.21272411X-RAY DIFFRACTION100
3.2703-3.41910.26591060.19652496X-RAY DIFFRACTION100
3.4191-3.59930.22861910.16672386X-RAY DIFFRACTION100
3.5993-3.82470.16071100.15982421X-RAY DIFFRACTION99
3.8247-4.11990.17051510.14412365X-RAY DIFFRACTION98
4.1199-4.53420.14021140.13242412X-RAY DIFFRACTION97
4.5342-5.18970.12841500.13632353X-RAY DIFFRACTION98
5.1897-6.53610.19881440.16822399X-RAY DIFFRACTION99
6.5361-49.5780.16671380.16512376X-RAY DIFFRACTION97
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)
11.55540.1519-0.21172.35580.73671.9042-0.0966-0.01620.08030.13760.03720.2590.087-0.14520.04130.27130.00330.04420.2440.04010.282713.662841.920790.8392
21.73270.4934-0.21321.8436-0.01721.5996-0.00690.24150.2035-0.1707-0.01920.1336-0.1389-0.15130.04170.26270.0060.00560.22440.02310.258116.491841.562281.4938
31.71980.0095-0.70382.1901-0.4632.42980.02780.39160.075-0.6396-0.01830.02740.2727-0.051-0.01930.6195-0.06810.04910.50710.00560.316726.552936.628153.6308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 226 )
2X-RAY DIFFRACTION2chain 'A' and (resid 227 through 414 )
3X-RAY DIFFRACTION3chain 'A' and (resid 415 through 588 )

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