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- PDB-5yko: Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain ... -

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Basic information

Entry
Database: PDB / ID: 5yko
TitleCrystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide
Components
  • H3(1-10)K4me3 peptide
  • Probable 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 / chromocenter / [histone H3]-trimethyl-L-lysine4 demethylase / : / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / plastid / negative regulation of gene expression, epigenetic / histone methyltransferase activity / developmental growth / histone demethylase activity / circadian rhythm / structural constituent of chromatin / nucleosome / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol
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. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Histone H3.1 / Lysine-specific demethylase JMJ14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
P: H3(1-10)K4me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5316
Polymers66,1942
Non-polymers3374
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-17 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.639, 100.113, 109.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Protein/peptide H3(1-10)K4me3 peptide


Mass: 1192.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM

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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: 2.84 Å3/Da / Density % sol: 56.68 %
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: May 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17462 / % possible obs: 99.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 13.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1702 / % possible all: 98.6

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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: 5YKN

5ykn


Resolution: 2.9→39.338 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2438 864 5.03 %
Rwork0.2037 --
obs0.2057 17179 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→39.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 13 0 4031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084138
X-RAY DIFFRACTIONf_angle_d0.9395600
X-RAY DIFFRACTIONf_dihedral_angle_d14.9861531
X-RAY DIFFRACTIONf_chiral_restr0.049578
X-RAY DIFFRACTIONf_plane_restr0.004722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.08170.3011550.27052637X-RAY DIFFRACTION98
3.0817-3.31950.30361400.24712661X-RAY DIFFRACTION99
3.3195-3.65340.27991520.22082684X-RAY DIFFRACTION100
3.6534-4.18150.2331320.18912731X-RAY DIFFRACTION100
4.1815-5.26630.18831260.16782759X-RAY DIFFRACTION100
5.2663-39.34160.22061590.19282843X-RAY DIFFRACTION99
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)
12.81811.1258-0.46182.1838-0.06082.1558-0.11280.1611-0.0933-0.14410.02-0.0350.1448-0.18690.10020.25050.07520.00420.2057-0.04710.338725.9924-21.4412-13.3707
21.64630.29760.0012.04020.02330.7543-0.06990.0960.1474-0.2497-0.0377-0.0001-0.1347-0.06370.11650.25090.01780.01220.24070.00550.2632.1114-5.83-12.1966
36.3579-1.6056-0.31423.25240.63792.32740.1459-0.04120.18490.0135-0.21130.2715-0.3244-0.37810.0640.4133-0.01690.00230.30190.04420.348228.393721.6898-10.2328
46.04010.485-0.79378.06463.78937.3795-0.00970.5242-0.3411-0.7017-0.14-0.24590.6271-0.69640.23281.01910.14350.09440.8789-0.331.430920.7535-3.211-8.2088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 245 )
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 478 )
3X-RAY DIFFRACTION3chain 'A' and (resid 479 through 588 )
4X-RAY DIFFRACTION4chain 'P' and (resid 1 through 7 )

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