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- PDB-6ip4: Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain ... -

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Basic information

Entry
Database: PDB / ID: 6ip4
TitleCrystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide
Components
  • Arabidopsis JMJ13
  • Histone H3.2
KeywordsGENE REGULATION / histone modification / flowering / epigenetics
Function / homology
Function and homology information


negative regulation of short-day photoperiodism, flowering / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / histone H3K27me2/H3K27me3 demethylase activity / flower development / chromocenter / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / 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 / plastid / negative regulation of gene expression, epigenetic ...negative regulation of short-day photoperiodism, flowering / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / histone H3K27me2/H3K27me3 demethylase activity / flower development / chromocenter / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / 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 / plastid / negative regulation of gene expression, epigenetic / response to temperature stimulus / histone demethylase activity / structural constituent of chromatin / nucleosome / histone binding / chromatin remodeling / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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. ...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 / Lysine-specific demethylase JMJ13 / Histone H3.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHu, H. / Du, J.
CitationJournal: Nat Commun / Year: 2019
Title: The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.
Authors: Zheng, S. / Hu, H. / Ren, H. / Yang, Z. / Qiu, Q. / Qi, W. / Liu, X. / Chen, X. / Cui, X. / Li, S. / Zhou, B. / Sun, D. / Cao, X. / Du, J.
History
DepositionNov 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _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: Arabidopsis JMJ13
B: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,47313
Polymers56,4642
Non-polymers1,00911
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-100 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.794, 128.794, 230.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-607-

SO4

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Arabidopsis JMJ13


Mass: 55335.070 Da / Num. of mol.: 1 / Fragment: UNP residues 90-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: F4KIX0
#2: Protein/peptide Histone H3.2 / Histone H3.1


Mass: 1129.311 Da / Num. of mol.: 1 / Fragment: UNP residues 25-36 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226

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Non-polymers , 5 types, 68 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / 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-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 4.89 Å3/Da / Density % sol: 74.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES, pH 6.5, 8% dioxane, and 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33189 / % possible obs: 93.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.091 / Net I/σ(I): 20.93
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 3316 / CC1/2: 0.615 / Rrim(I) all: 0.953 / Rsym value: 0.868 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IP0

6ip0


Resolution: 2.6→49.367 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2465 1681 5.06 %
Rwork0.2128 --
obs0.2146 33189 93.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 48 57 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013925
X-RAY DIFFRACTIONf_angle_d1.3025323
X-RAY DIFFRACTIONf_dihedral_angle_d25.5711422
X-RAY DIFFRACTIONf_chiral_restr0.083573
X-RAY DIFFRACTIONf_plane_restr0.009672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5983-2.67480.30151370.27962614X-RAY DIFFRACTION95
2.6748-2.76110.29851360.28342613X-RAY DIFFRACTION95
2.7611-2.85980.32031340.27522636X-RAY DIFFRACTION95
2.8598-2.97420.28831400.25272616X-RAY DIFFRACTION95
2.9742-3.10960.26911330.24672613X-RAY DIFFRACTION94
3.1096-3.27350.28251250.23882632X-RAY DIFFRACTION94
3.2735-3.47850.2961390.23052617X-RAY DIFFRACTION94
3.4785-3.7470.30241410.21142611X-RAY DIFFRACTION94
3.747-4.12390.21271600.18872610X-RAY DIFFRACTION93
4.1239-4.72030.21361510.16992610X-RAY DIFFRACTION92
4.7203-5.94550.21971400.1972627X-RAY DIFFRACTION91
5.9455-49.37570.24131450.22282709X-RAY DIFFRACTION88
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)
12.7649-0.184-0.4223.9448-0.04683.876-0.2222-0.36620.06760.31490.2098-0.21320.17130.2995-0.00860.75170.40940.00310.4650.00190.738941.626745.0074140.6084
21.9207-1.3661-0.32494.54530.78412.19-0.4377-0.56330.10650.56370.4297-0.40940.11110.114900.76180.3938-0.05230.6095-0.04910.793944.085944.9932142.2435
35.62920.7911-6.92662.0639-0.64448.94041.1792-0.99150.9276-0.2894-0.4121-2.1896-0.56612.1187-0.57821.28910.3888-0.10061.349-0.20821.985464.958349.7549139.7602
42.7655-1.93870.19413.73760.23582.5401-0.0318-0.02250.3592-0.25470.1048-0.6922-0.07990.1988-0.0790.73790.2950.02020.4286-0.00260.870648.534343.2432132.9766
51.9249-1.9063-1.11385.9618-1.10252.1617-0.14030.2573-0.44870.01370.1120.4280.815-0.0110.05010.88640.21540.12960.4168-0.06120.954546.990821.6332125.7246
63.5871-0.78270.97162.36750.14532.9646-0.4253-0.0686-0.1160.10490.0757-0.2678-0.23890.0150.34131.00980.16960.15210.2931-0.00870.861461.144614.1821127.0798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 187 through 333 )
3X-RAY DIFFRACTION3chain 'A' and (resid 334 through 358 )
4X-RAY DIFFRACTION4chain 'A' and (resid 359 through 421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 453 )
6X-RAY DIFFRACTION6chain 'A' and (resid 454 through 563 )

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