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- PDB-2qqs: JMJD2A tandem tudor domains in complex with a trimethylated histo... -

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Basic information

Entry
Database: PDB / ID: 2qqs
TitleJMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide
Components
  • JmjC domain-containing histone demethylation protein 3A
  • METHYLATED HISTONE H4 PEPTIDE
KeywordsOXIDOREDUCTASE / HISTONE LYSINE DEMETHYLASE / METAL BINDING PROTEIN / PROTEIN-METHYLATED PEPTIDE COMPLEX / Chromatin regulator / Dioxygenase / Host-virus interaction / Iron / Metal-binding / Nucleus / Phosphorylation / Polymorphism / Transcription / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / negative regulation of autophagy / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / fibrillar center / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / chromatin organization / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #70 / : / : / : / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 ...Vcp-like ATPase; Chain A, domain 2 - #70 / : / : / : / Vcp-like ATPase; Chain A, domain 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / 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. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 4A / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsLee, J. / Botuyan, M.V. / Mer, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor.
Authors: Lee, J. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JmjC domain-containing histone demethylation protein 3A
B: JmjC domain-containing histone demethylation protein 3A
C: METHYLATED HISTONE H4 PEPTIDE
D: METHYLATED HISTONE H4 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)29,6514
Polymers29,6514
Non-polymers00
Water1,13563
1
A: JmjC domain-containing histone demethylation protein 3A
D: METHYLATED HISTONE H4 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)14,8252
Polymers14,8252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JmjC domain-containing histone demethylation protein 3A
C: METHYLATED HISTONE H4 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)14,8252
Polymers14,8252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.970, 27.689, 82.424
Angle α, β, γ (deg.)90.00, 90.77, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is made of one molecule of JMJD2A and one molecule of methylated histone H4.

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Components

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


Mass: 13455.816 Da / Num. of mol.: 2 / Fragment: JMJD2A HYBRID TUDOR DOMAINS (residues: 897-1011)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2A, JHDM3A, JMJD2, KIAA0677 / Plasmid: pTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
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 METHYLATED HISTONE H4 PEPTIDE


Mass: 1369.662 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic methyalted histone H4 peptide derived from human sequence.
References: UniProt: P62805*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 293 K / Details: 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 5184 / % possible obs: 88.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.2
Reflection shellResolution: 2.82→2.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QQR

2qqr


Resolution: 2.82→25.97 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.824 / SU B: 16.388 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28292 237 4.4 %RANDOM
Rwork0.23612 ---
obs0.23811 5184 85.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20.24 Å2
2---0.66 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.82→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 0 63 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9382580
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8355225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2324.34106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.07115308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9421513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021483
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.2908
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21267
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4941.51146
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85821838
X-RAY DIFFRACTIONr_scbond_it1.4563840
X-RAY DIFFRACTIONr_scangle_it2.0314.5742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.82→2.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.8 13 -
Rwork0.563 264 -
obs--60.48 %

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