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- PDB-2q8c: Crystal structure of JMJD2A in ternary complex with an histone H3... -

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Basic information

Entry
Database: PDB / ID: 2q8c
TitleCrystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate
Components
  • HISTONE 3 PEPTIDE
  • JmjC domain-containing histone demethylation protein 3A
KeywordsOXIDOREDUCTASE / histone demethylase / hydroxylase / jumonji
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / 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. / Cupin / 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 / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsCouture, J.-F. / Collazo, E. / Ortiz-Tello, P. / Brunzelle, J.S. / Trievel, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase.
Authors: Couture, J.F. / Collazo, E. / Ortiz-Tello, P.A. / Brunzelle, J.S. / Trievel, R.C.
History
DepositionJun 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 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 / struct_ref_seq_dif / 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.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 / _struct_ref_seq_dif.details / _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: JmjC domain-containing histone demethylation protein 3A
B: JmjC domain-containing histone demethylation protein 3A
F: HISTONE 3 PEPTIDE
G: HISTONE 3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,48310
Polymers84,9434
Non-polymers5406
Water3,585199
1
A: JmjC domain-containing histone demethylation protein 3A
F: HISTONE 3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7425
Polymers42,4712
Non-polymers2703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-13 kcal/mol
Surface area15720 Å2
MethodPISA
2
B: JmjC domain-containing histone demethylation protein 3A
G: HISTONE 3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7425
Polymers42,4712
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.887, 149.121, 57.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein is active as a monomer with two molecules in the asymmetric unit.

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABFG

#1: Protein JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A


Mass: 40863.504 Da / Num. of mol.: 2 / Fragment: Jumonji domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2A, JHDM3A, JMJD2, KIAA0677 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21De3pLysS
References: UniProt: O75164, 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 HISTONE 3 PEPTIDE


Mass: 1607.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide

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Non-polymers , 4 types, 205 molecules

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


Mass: 58.693 Da / Num. of mol.: 2 / 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-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.58 Å3/Da / Density % sol: 52.36 %

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→28.9 Å / Num. obs: 54585 / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.03 / Net I/σ(I): 39
Reflection shellResolution: 2.04→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5039 / Rsym value: 0.476

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gp5

2gp5


Resolution: 2.047→28.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.563 / SU ML: 0.123 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.191 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23584 2762 5.1 %RANDOM
Rwork0.20115 ---
obs0.20296 54535 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.893 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.047→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5607 0 24 199 5830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225816
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9457879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55822.989281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07615943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6161540
X-RAY DIFFRACTIONr_chiral_restr0.0890.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024517
X-RAY DIFFRACTIONr_nbd_refined0.2020.22622
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2279
X-RAY DIFFRACTIONr_metal_ion_refined0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.26
X-RAY DIFFRACTIONr_mcbond_it0.6911.53560
X-RAY DIFFRACTIONr_mcangle_it1.12825563
X-RAY DIFFRACTIONr_scbond_it1.66232655
X-RAY DIFFRACTIONr_scangle_it2.4674.52316
LS refinement shellResolution: 2.047→2.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 178 -
Rwork0.266 3439 -
obs--90.65 %

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