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- PDB-3gl6: Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 3gl6
TitleCrystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide
Components
  • Histone H3
  • Histone demethylase JARID1A
KeywordsOXIDOREDUCTASE / PHD finger / H3(1-9)K4me3 peptide / leukemia / Alternative splicing / Chromatin regulator / Developmental protein / Dioxygenase / Iron / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / Zinc / Zinc-finger / Chromosomal protein / DNA-binding / Nucleosome core
Function / homology
Function and homology information


facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding ...facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding / structural constituent of chromatin / nucleosome / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / 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, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Lysine-specific demethylase 5A / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Z. / Song, J. / Patel, D.J.
CitationJournal: Nature / Year: 2009
Title: Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.
Authors: Wang, G.G. / Song, J. / Wang, Z. / Dormann, H.L. / Casadio, F. / Li, H. / Luo, J.L. / Patel, D.J. / Allis, C.D.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone demethylase JARID1A
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1045
Polymers6,9082
Non-polymers1963
Water57632
1
A: Histone demethylase JARID1A
B: Histone H3
hetero molecules

A: Histone demethylase JARID1A
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,20810
Polymers13,8164
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1,-y-1,z1
Buried area4010 Å2
ΔGint-20 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.950, 49.950, 86.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding protein 2 / RBBP-2


Mass: 5802.490 Da / Num. of mol.: 1 / Fragment: C-terminal PHD finger
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID1A, RBBP2, RBP2 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P29375, 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 H3


Mass: 1105.334 Da / Num. of mol.: 1 / Fragment: Histone H3 N-terminal residues 1-9 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: PDB-PDB, UniProt: Q92133*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11971
21971
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97949
SYNCHROTRONAPS 24-ID-C21.28215
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 5, 2008
ADSC QUANTUM 3152CCDMar 20, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI mirrorsSINGLE WAVELENGTHMx-ray1
2SI mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
21.282151
ReflectionResolution: 1.9→50 Å / Num. all: 8377 / Num. obs: 8172 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 55.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 6.46 / Num. unique all: 714 / Rsym value: 0.18 / % possible all: 85.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 786 -Random
Rwork0.208 ---
all0.229 8377 --
obs0.222 8172 97.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 0 3 32 501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.32 66 -
Rwork0.27 --
obs-696 85.1 %

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