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- PDB-7vyw: Crystal structure of the chromodomain of Arabidopsis LHP1 in comp... -

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Basic information

Entry
Database: PDB / ID: 7vyw
TitleCrystal structure of the chromodomain of Arabidopsis LHP1 in complex with methylated histone H3K9 peptide
Components
  • Chromo domain-containing protein LHP1
  • methylated histone H3K9 peptide
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


vernalization response / shoot system morphogenesis / photoperiodism / GTP cyclohydrolase II activity / multidimensional cell growth / negative regulation of flower development / photoperiodism, flowering / flower development / negative regulation of gene expression, epigenetic / : ...vernalization response / shoot system morphogenesis / photoperiodism / GTP cyclohydrolase II activity / multidimensional cell growth / negative regulation of flower development / photoperiodism, flowering / flower development / negative regulation of gene expression, epigenetic / : / heterochromatin / chloroplast / euchromatin / heterochromatin formation / chromatin organization / sequence-specific DNA binding / cell differentiation / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / identical protein binding / nucleus
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
Similarity search - Domain/homology
Chromo domain-containing protein LHP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Zhang, M. / Min, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500615 China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain.
Authors: Liu, Y. / Yang, X. / Zhou, M. / Yang, Y. / Li, F. / Yan, X. / Zhang, M. / Wei, Z. / Qin, S. / Min, J.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromo domain-containing protein LHP1
B: methylated histone H3K9 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5805
Polymers7,2912
Non-polymers2883
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-30 kcal/mol
Surface area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.088, 28.547, 70.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromo domain-containing protein LHP1


Mass: 6574.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q946J8
#2: Protein/peptide methylated histone H3K9 peptide


Mass: 716.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.75 Å3/Da / Density % sol: 29.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes, pH 7.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→35.26 Å / Num. obs: 6673 / % possible obs: 90.29 % / Redundancy: 4.6 % / Biso Wilson estimate: 10.57 Å2 / CC1/2: 0.982 / Net I/σ(I): 23.2
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 294 / CC1/2: 0.968

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3L

1q3l


Resolution: 1.6→35.26 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 335 5.02 %
Rwork0.182 6338 -
obs0.1843 6673 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.2 Å2 / Biso mean: 9.8733 Å2 / Biso min: 1.8 Å2
Refinement stepCycle: final / Resolution: 1.6→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms437 0 15 59 511
Biso mean--22.06 19.04 -
Num. residues----53
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.24551670.18113044321189
2.02-35.260.22421680.18243294346292

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