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- PDB-4pll: Structure of the chromodaomain of MRG2 in complex with H3K36me3 -

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Basic information

Entry
Database: PDB / ID: 4pll
TitleStructure of the chromodaomain of MRG2 in complex with H3K36me3
Components
  • At1g02740
  • H3K36me3
KeywordsTRANSCRIPTION / chromodomain / H3K36me3
Function / homology
Function and homology information


euchromatin binding / regulation of long-day photoperiodism, flowering / rDNA protrusion / regulation of timing of transition from vegetative to reproductive phase / epigenetic regulation of gene expression / methylated histone binding / promoter-specific chromatin binding / structural constituent of chromatin / : / nucleosome ...euchromatin binding / regulation of long-day photoperiodism, flowering / rDNA protrusion / regulation of timing of transition from vegetative to reproductive phase / epigenetic regulation of gene expression / methylated histone binding / promoter-specific chromatin binding / structural constituent of chromatin / : / nucleosome / protein heterodimerization activity / nucleolus / regulation of DNA-templated transcription / DNA binding / nucleus / plasma membrane
Similarity search - Function
Agenet domain, plant type / Tudor-like domain present in plant sequences. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain ...Agenet domain, plant type / Tudor-like domain present in plant sequences. / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / SH3 type barrels. - #140 / Chromo-like domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / SH3 type barrels. / Histone-fold / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H3.3 / Protein MRG2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, Y. / Huang, Y.
CitationJournal: Plos Genet. / Year: 2014
Title: Regulation of arabidopsis flowering by the histone mark readers MRG1/2 via interaction with CONSTANS to modulate FT expression.
Authors: Bu, Z. / Yu, Y. / Li, Z. / Liu, Y. / Jiang, W. / Huang, Y. / Dong, A.W.
History
DepositionMay 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: At1g02740
B: At1g02740
C: H3K36me3
D: H3K36me3


Theoretical massNumber of molelcules
Total (without water)20,7554
Polymers20,7554
Non-polymers00
Water1448
1
A: At1g02740
C: H3K36me3


Theoretical massNumber of molelcules
Total (without water)10,3782
Polymers10,3782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-4 kcal/mol
Surface area4050 Å2
MethodPISA
2
B: At1g02740
D: H3K36me3


Theoretical massNumber of molelcules
Total (without water)10,3782
Polymers10,3782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-5 kcal/mol
Surface area4170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.157, 109.157, 29.977
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein At1g02740 / MRG family protein


Mass: 9118.196 Da / Num. of mol.: 2 / Fragment: UNP residues 51-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g02740 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4V3E2
#2: Protein/peptide H3K36me3 /


Mass: 1259.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: P59169*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MES pH 6.5, 30% polyethylene glycol monomethyl ether 5000, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 6489 / % possible obs: 99.07 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 31
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.4 / % possible all: 97.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.575 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 32.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 644 9.92 %
Rwork0.2399 --
obs0.2437 6489 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→28.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 8 1028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011055
X-RAY DIFFRACTIONf_angle_d1.331418
X-RAY DIFFRACTIONf_dihedral_angle_d19.901372
X-RAY DIFFRACTIONf_chiral_restr0.059134
X-RAY DIFFRACTIONf_plane_restr0.006170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80050.37471180.31951139X-RAY DIFFRACTION97
2.8005-3.08210.32521290.30731138X-RAY DIFFRACTION99
3.0821-3.52730.27931300.26351166X-RAY DIFFRACTION100
3.5273-4.44140.26521310.21661174X-RAY DIFFRACTION100
4.4414-28.57640.26381360.22051228X-RAY DIFFRACTION100

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