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- PDB-4pli: Structure of the chromodomain of MRG2 in complex with H3K36me3 -

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Basic information

Entry
Database: PDB / ID: 4pli
TitleStructure of the chromodomain of MRG2 in complex with H3K36me3
Components
  • At1g02740
  • H3K36me3
KeywordsTRANSCRIPTION / chromodamian / H3k36me3
Function / homology
Function and homology information


regulation of long-day photoperiodism, flowering / euchromatin binding / rDNA protrusion / regulation of timing of transition from vegetative to reproductive phase / methylated histone binding / epigenetic regulation of gene expression / promoter-specific chromatin binding / structural constituent of chromatin / nucleosome / protein heterodimerization activity ...regulation of long-day photoperiodism, flowering / euchromatin binding / rDNA protrusion / regulation of timing of transition from vegetative to reproductive phase / methylated histone binding / epigenetic regulation of gene expression / promoter-specific chromatin binding / structural constituent of chromatin / nucleosome / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / DNA binding / nucleus / plasma membrane
Similarity search - Function
Agenet domain, plant type / Tudor-like domain present in plant sequences. / : / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain ...Agenet domain, plant type / Tudor-like domain present in plant sequences. / : / MSL3 chromodomain-like / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / 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: 1.651 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 1.1Nov 4, 2015Group: Experimental preparation
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Dec 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
Water1,65792
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-5 kcal/mol
Surface area4210 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 area4270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.325, 54.325, 127.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M HEPES pH 7.5, 10% PEG 8000, 8% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 25190 / % possible obs: 98.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 47.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.438 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.651→24.997 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2005 7.96 %
Rwork0.2104 --
obs0.212 25190 98.61 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→24.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 0 92 1124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071096
X-RAY DIFFRACTIONf_angle_d1.0051483
X-RAY DIFFRACTIONf_dihedral_angle_d14.37395
X-RAY DIFFRACTIONf_chiral_restr0.049144
X-RAY DIFFRACTIONf_plane_restr0.004179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.651-1.69250.23851460.22121655X-RAY DIFFRACTION99
1.6925-1.73820.25921460.21941647X-RAY DIFFRACTION100
1.7382-1.78940.23091430.20391664X-RAY DIFFRACTION100
1.7894-1.84710.18941510.21531686X-RAY DIFFRACTION100
1.8471-1.91310.22751450.19981668X-RAY DIFFRACTION100
1.9131-1.98970.2431430.19131688X-RAY DIFFRACTION100
1.9897-2.08020.21991410.19911685X-RAY DIFFRACTION100
2.0802-2.18980.21141370.19821694X-RAY DIFFRACTION100
2.1898-2.32690.22311450.21491661X-RAY DIFFRACTION100
2.3269-2.50640.25181440.21731682X-RAY DIFFRACTION100
2.5064-2.75830.23811480.21891684X-RAY DIFFRACTION100
2.7583-3.15680.22511440.21831693X-RAY DIFFRACTION100
3.1568-3.97470.21831390.20861595X-RAY DIFFRACTION95
3.9747-25.00020.24241330.21021483X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 3.5228 Å / Origin y: -7.3003 Å / Origin z: -18.2901 Å
111213212223313233
T0.1619 Å2-0.01 Å2-0.0098 Å2-0.1878 Å2-0.0159 Å2--0.1939 Å2
L1.0594 °20.8958 °20.6117 °2-0.9248 °20.1795 °2--1.1777 °2
S-0.034 Å °0.02 Å °0.1421 Å °-0.0209 Å °-0.072 Å °0.0765 Å °0.0259 Å °0.0436 Å °0.0959 Å °
Refinement TLS groupSelection details: all

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