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- PDB-4igq: Histone H3 Lysine 4 Demethylating Rice JMJ703 in complex with met... -

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Basic information

Entry
Database: PDB / ID: 4igq
TitleHistone H3 Lysine 4 Demethylating Rice JMJ703 in complex with methylated H3K4 substrate
Components
  • Os05g0196500 protein
  • mathylated H3K4 substrate
KeywordsSTRUCTURAL PROTEIN/TRANSCRIPTION / JumonjiC / Histone demethylase / STRUCTURAL PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


positive regulation of growth rate / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / negative regulation of gene expression, epigenetic / ferrous iron binding / regulation of gene expression / chromatin remodeling / chromatin / nucleus
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 / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Lysine-specific demethylase JMJ703
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChen, Q.F. / Chen, X.S. / Wang, Q. / Zhang, F.B. / Lou, Z.Y. / Zhang, Q.F. / Zhou, D.X.
CitationJournal: PLoS Genet. / Year: 2013
Title: Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice.
Authors: Chen, Q. / Chen, X. / Wang, Q. / Zhang, F. / Lou, Z. / Zhang, Q. / Zhou, D.X.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_site
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.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.pdbx_leaving_atom_flag / _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_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: Os05g0196500 protein
B: mathylated H3K4 substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5894
Polymers41,3872
Non-polymers2032
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-17 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.425, 91.425, 75.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

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Components

#1: Protein Os05g0196500 protein / Putative uncharacterized protein P0617H07.8 / Histone H3


Mass: 40968.012 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 139-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: P0617H07.8, Os05g0196500 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53WJ1
#2: Protein/peptide mathylated H3K4 substrate


Mass: 418.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: potassium phosphate monobasic, 25% (w/v) polyethylene glycol 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 15151 / Num. obs: 15108 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ6

2oq6


Resolution: 2.35→39.588 Å / SU ML: 0.55 / σ(F): 0.87 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 811 5.04 %random
Rwork0.1811 ---
all0.1886 15151 --
obs0.1837 15108 99.78 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.804 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4367 Å20 Å2-0 Å2
2--0.4367 Å20 Å2
3----0.8734 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 11 141 2408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082333
X-RAY DIFFRACTIONf_angle_d1.2253169
X-RAY DIFFRACTIONf_dihedral_angle_d16.543844
X-RAY DIFFRACTIONf_chiral_restr0.092322
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3001-2.44420.25121470.20442504
2.4442-2.63290.26451380.20352540
2.6329-2.89780.26561400.19642511
2.8978-3.31690.27431300.18312553
3.3169-4.17830.20261400.16232549
4.1783-39.5940.21541160.17872609

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