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- PDB-4pl6: Structure of the chromodomain of MRG2 in complex with H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 4pl6
TitleStructure of the chromodomain of MRG2 in complex with H3K4me3
Components
  • At1g02740
  • H3K4me3
KeywordsTRANSCRIPTION / chromo domain / H3K4me3
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 / Resolution: 1.681 Å
AuthorsLiu, Y.C. / 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 16, 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: H3K4me3
D: H3K4me3


Theoretical massNumber of molelcules
Total (without water)20,8234
Polymers20,8234
Non-polymers00
Water2,378132
1
A: At1g02740
C: H3K4me3


Theoretical massNumber of molelcules
Total (without water)10,4122
Polymers10,4122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-5 kcal/mol
Surface area4300 Å2
MethodPISA
2
B: At1g02740
D: H3K4me3


Theoretical massNumber of molelcules
Total (without water)10,4122
Polymers10,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-5 kcal/mol
Surface area4190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.231, 54.231, 127.922
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 H3K4me3 /


Mass: 1293.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59169*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, PH 7.5, 9% PEG 6K, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. obs: 23375 / % possible obs: 96.6 % / Redundancy: 3.3 % / Net I/σ(I): 36.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.681→24.965 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 1962 8.39 %
Rwork0.1905 --
obs0.1925 23374 96.62 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.681→24.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 0 132 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061079
X-RAY DIFFRACTIONf_angle_d0.961454
X-RAY DIFFRACTIONf_dihedral_angle_d16.257384
X-RAY DIFFRACTIONf_chiral_restr0.052139
X-RAY DIFFRACTIONf_plane_restr0.004175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.681-1.72280.34551320.27991480X-RAY DIFFRACTION94
1.7228-1.76940.30531410.23991487X-RAY DIFFRACTION94
1.7694-1.82140.281370.21821534X-RAY DIFFRACTION97
1.8214-1.88020.23571440.20671558X-RAY DIFFRACTION97
1.8802-1.94740.21941420.20381544X-RAY DIFFRACTION99
1.9474-2.02530.1921460.19071542X-RAY DIFFRACTION98
2.0253-2.11750.2041420.18171553X-RAY DIFFRACTION99
2.1175-2.2290.23891350.18741569X-RAY DIFFRACTION99
2.229-2.36860.23951420.20381581X-RAY DIFFRACTION99
2.3686-2.55130.20891450.20821542X-RAY DIFFRACTION99
2.5513-2.80770.24361490.21171560X-RAY DIFFRACTION99
2.8077-3.21330.22921410.18871553X-RAY DIFFRACTION97
3.2133-4.04560.19061400.17711500X-RAY DIFFRACTION95
4.0456-24.96750.18151260.17071409X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 3.3538 Å / Origin y: -7.2763 Å / Origin z: -18.5091 Å
111213212223313233
T0.1374 Å2-0.0187 Å2-0.0076 Å2-0.1533 Å2-0.0133 Å2--0.1578 Å2
L0.4475 °20.4715 °20.3333 °2-0.4914 °20.1957 °2--0.7861 °2
S-0.0407 Å °-0.0274 Å °0.0514 Å °-0.0264 Å °-0.0389 Å °0.0402 Å °0.0603 Å °0.0537 Å °0 Å °
Refinement TLS groupSelection details: all

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