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- PDB-8xag: Crystal structure of the chromodomain of Arabidopsis LHP1 in comp... -

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Basic information

Entry
Database: PDB / ID: 8xag
TitleCrystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone H3.3K27me3 peptide
Components
  • Chromo domain-containing protein LHP1
  • histone H3.3K27me3 peptide
KeywordsGENE REGULATION / LHP1 / H3.3K27me3
Function / homology
Function and homology information


rDNA protrusion / photoperiodism / vernalization response / shoot system morphogenesis / negative regulation of flower development / GTP cyclohydrolase II activity / multidimensional cell growth / photoperiodism, flowering / flower development / negative regulation of gene expression, epigenetic ...rDNA protrusion / photoperiodism / vernalization response / shoot system morphogenesis / negative regulation of flower development / GTP cyclohydrolase II activity / multidimensional cell growth / photoperiodism, flowering / flower development / negative regulation of gene expression, epigenetic / heterochromatin / : / chloroplast / euchromatin / structural constituent of chromatin / nucleosome / heterochromatin formation / chromatin organization / sequence-specific DNA binding / cell differentiation / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / DNA binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Chromo domain-containing protein LHP1 / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain ...Chromo domain-containing protein LHP1 / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / 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 / Histone-fold
Similarity search - Domain/homology
Histone H3.3 / Chromo domain-containing protein LHP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLiu, Y. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
CitationJournal: To Be Published
Title: Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone H3.3K27me3 peptide
Authors: Liu, Y. / Huang, Y.
History
DepositionDec 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromo domain-containing protein LHP1
B: Chromo domain-containing protein LHP1
C: histone H3.3K27me3 peptide
D: histone H3.3K27me3 peptide


Theoretical massNumber of molelcules
Total (without water)17,1214
Polymers17,1214
Non-polymers00
Water3,189177
1
A: Chromo domain-containing protein LHP1
C: histone H3.3K27me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,5612
Polymers8,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area5340 Å2
MethodPISA
2
B: Chromo domain-containing protein LHP1
D: histone H3.3K27me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,5612
Polymers8,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area5360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.370, 90.623, 63.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

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Components

#1: Protein Chromo domain-containing protein LHP1


Mass: 7685.710 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q946J8
#2: Protein/peptide histone H3.3K27me3 peptide / Histone H3.2


Mass: 875.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59169
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate pH 5.6, 20% PEG 4000, 16% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 18308 / % possible obs: 94.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 30.4
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.483 / Num. unique obs: 1707

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→27.42 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.5746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2504 1827 10 %
Rwork0.2274 16445 -
obs0.2297 18272 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.84 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 177 1269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281116
X-RAY DIFFRACTIONf_angle_d0.65061508
X-RAY DIFFRACTIONf_chiral_restr0.0435156
X-RAY DIFFRACTIONf_plane_restr0.0031190
X-RAY DIFFRACTIONf_dihedral_angle_d6.4759154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.40481160.36151050X-RAY DIFFRACTION79.37
1.8-1.850.35371380.32711241X-RAY DIFFRACTION93.24
1.85-1.910.34871420.30621262X-RAY DIFFRACTION94.93
1.91-1.980.31651400.26791268X-RAY DIFFRACTION95.72
1.98-2.060.26811410.27351262X-RAY DIFFRACTION94.35
2.06-2.150.28651380.23031238X-RAY DIFFRACTION93.86
2.15-2.260.26641420.23231270X-RAY DIFFRACTION94.51
2.26-2.40.27451380.23311245X-RAY DIFFRACTION93.32
2.4-2.590.30411380.24411254X-RAY DIFFRACTION93.42
2.59-2.850.30721420.23721278X-RAY DIFFRACTION93.73
2.85-3.260.22521440.22781296X-RAY DIFFRACTION94.86
3.26-4.10.19551480.19621338X-RAY DIFFRACTION98.09
4.11-27.420.20951600.19481443X-RAY DIFFRACTION99.69

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