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- PDB-5eq0: Crystal Structure of chromodomain of CBX8 in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 5eq0
TitleCrystal Structure of chromodomain of CBX8 in complex with inhibitor UNC3866
Components
  • Chromobox protein homolog 8
  • unc3866
Keywordstranscription/transcription inhibitor / structural genomics / Structural Genomics Consortium / SGC / transcription-transcription inhibitor complex
Function / homology
Function and homology information


PRC1 complex / ubiquitin-protein transferase activator activity / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of collagen biosynthetic process / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding ...PRC1 complex / ubiquitin-protein transferase activator activity / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of collagen biosynthetic process / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / cellular response to hydrogen peroxide / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / chromatin binding / positive regulation of cell population proliferation / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain ...CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNC3866 / Chromobox protein homolog 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.18 Å
AuthorsLiu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.
Authors: Stuckey, J.I. / Dickson, B.M. / Cheng, N. / Liu, Y. / Norris, J.L. / Cholensky, S.H. / Tempel, W. / Qin, S. / Huber, K.G. / Sagum, C. / Black, K. / Li, F. / Huang, X.P. / Roth, B.L. / ...Authors: Stuckey, J.I. / Dickson, B.M. / Cheng, N. / Liu, Y. / Norris, J.L. / Cholensky, S.H. / Tempel, W. / Qin, S. / Huber, K.G. / Sagum, C. / Black, K. / Li, F. / Huang, X.P. / Roth, B.L. / Baughman, B.M. / Senisterra, G. / Pattenden, S.G. / Vedadi, M. / Brown, P.J. / Bedford, M.T. / Min, J. / Arrowsmith, C.H. / James, L.I. / Frye, S.V.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 2.0Nov 27, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 8
B: unc3866


Theoretical massNumber of molelcules
Total (without water)7,46314
Polymers7,4632
Non-polymers012
Water88349
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-7 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.575, 30.007, 36.104
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number4
Space group name H-MP1211
Detailsauthors have not specified the biological unit

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Components

#1: Protein Chromobox protein homolog 8 / Polycomb 3 homolog / hPc3 / Rectachrome 1


Mass: 6667.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX8, PC3, RC1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9HC52
#2: Protein/peptide unc3866


Type: Oligopeptide / Class: Inhibitor / Mass: 795.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) Homo sapiens (human) / References: UNC3866
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.2 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M sodium citrate, 0.1 M HEPES, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786036 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786036 Å / Relative weight: 1
ReflectionResolution: 1.18→35.54 Å / Num. obs: 21328 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 20.5
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementResolution: 1.18→35.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.19 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH COORDINATES DERIVED FROM A SIMILAR COMPLEX OF CBX7 AND DATA FROM AN ISOMORPHOUS CRYSTAL. PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH COORDINATES DERIVED FROM A SIMILAR COMPLEX OF CBX7 AND DATA FROM AN ISOMORPHOUS CRYSTAL. PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING WERE PERFORMED BY ARP/WARP. PHENIX.ELBOW/MOGUL WAS USED TO GENERATE GEOMETRY RESTRAINTS FOR INHIBITOR BUILDING BLOCKS. JLIGAND WAS USED FOR PREPARATION OF LINK RESTRAINTS. LINK RESTRAINTS WERE MANUALLY MODIFIED, FOR EXAMPLE TO RESTRAIN PLANAR GEOMETRY OF METHYL ESTER TERMINUS OF INHIBITOR. ELECTRON DENSITY PEAKS NEAR CBX8 RESIDUES K23 AND R52, RESPECTIVELY, SUGGEST PRESENCE OF PHOSPHATE OR SULFATE IONS, BUT WE COULD NOT EXPLAIN THE ORIGIN OF SUCH IONS. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY. ADP WERE ANALYZED ON THE PARVATI SERVER.
RfactorNum. reflection% reflection
Rfree0.186 1069 5 %
Rwork0.156 --
obs0.158 20239 99.5 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.18 Å2
2---0.26 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.18→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms525 0 12 49 586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.019586
X-RAY DIFFRACTIONr_bond_other_d0.0030.02592
X-RAY DIFFRACTIONr_angle_refined_deg1.961.964791
X-RAY DIFFRACTIONr_angle_other_deg1.09831357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.317567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.54421.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97615114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.716159
X-RAY DIFFRACTIONr_chiral_restr0.1250.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02151
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2570.887257
X-RAY DIFFRACTIONr_mcbond_other1.2550.883254
X-RAY DIFFRACTIONr_mcangle_it1.7771.335321
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.87731178
X-RAY DIFFRACTIONr_sphericity_free21.278520
X-RAY DIFFRACTIONr_sphericity_bonded8.89251202
LS refinement shellResolution: 1.18→1.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 50 -
Rwork0.176 1481 -
obs--97.89 %

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