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- PDB-7vrf: Crystal structure of Oxpecker chromodomain in complex with H3K9me3 -

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Basic information

Entry
Database: PDB / ID: 7vrf
TitleCrystal structure of Oxpecker chromodomain in complex with H3K9me3
Components
  • H3K9me3
  • Oxpecker
KeywordsGENE REGULATION / chromodomain / histone binding
Function / homology
Function and homology information


Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA ...Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / chromosome organization / pericentric heterochromatin / nucleosomal DNA binding / methylated histone binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / chromatin binding / chromatin / nucleus
Similarity search - Function
: / : / Chromo domain subgroup / 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. ...: / : / Chromo domain subgroup / 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
Oxpecker / Histone H3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHuang, Y. / Jin, Z. / Yu, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural insights into the chromodomain of Oxpecker in complex with histone H3 lysine 9 trimethylation reveal a transposon silencing mechanism by heterodimerization.
Authors: Jin, Z. / Yu, B. / Huang, Y.
History
DepositionOct 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Oxpecker
B: Oxpecker
C: H3K9me3
D: H3K9me3


Theoretical massNumber of molelcules
Total (without water)19,5364
Polymers19,5364
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-23 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.421, 37.455, 38.757
Angle α, β, γ (deg.)61.228, 88.787, 74.943
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Oxpecker


Mass: 8560.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Oxp, Dmel\CG18186, OXP, CG18186, Dmel_CG18186 / Production host: Escherichia coli (E. coli) / References: UniProt: A1ZAW9
#2: Protein/peptide H3K9me3


Mass: 1207.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P02299
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium citrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 15565 / % possible obs: 95.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.19 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.8
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.233 / Num. unique obs: 752

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX1.18.2_3874refinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U68

4u68


Resolution: 1.7→25.72 Å / SU ML: 0.1369 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 27.8653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 1549 9.96 %
Rwork0.192 14005 -
obs0.1965 15554 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 0 97 1252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161179
X-RAY DIFFRACTIONf_angle_d1.29841586
X-RAY DIFFRACTIONf_chiral_restr0.0597161
X-RAY DIFFRACTIONf_plane_restr0.0072198
X-RAY DIFFRACTIONf_dihedral_angle_d21.5314165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.26291310.21341214X-RAY DIFFRACTION90.39
1.76-1.820.24691470.20491249X-RAY DIFFRACTION95.55
1.82-1.890.26121430.20531287X-RAY DIFFRACTION95.21
1.89-1.980.29661350.21491282X-RAY DIFFRACTION95.49
1.98-2.080.2681430.21561295X-RAY DIFFRACTION95.8
2.08-2.210.23551440.20391255X-RAY DIFFRACTION95.43
2.21-2.380.23271450.20091276X-RAY DIFFRACTION96.21
2.38-2.620.26611430.22781316X-RAY DIFFRACTION97.33
2.62-30.26951430.22341285X-RAY DIFFRACTION97.01
3-3.780.24131350.18341279X-RAY DIFFRACTION94.58
3.78-25.720.19611400.15611267X-RAY DIFFRACTION95.13

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