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- PDB-5epk: Crystal Structure of chromodomain of CBX2 in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 5epk
TitleCrystal Structure of chromodomain of CBX2 in complex with inhibitor UNC3866
Components
  • Chromobox protein homolog 2
  • unc3866
Keywordstranscription/transcription inhibitor / structural genomics / Structural Genomics Consortium / SGC / transcription-transcription inhibitor complex
Function / homology
Function and homology information


development of primary sexual characteristics / PRC1 complex / 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 / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding / SUMOylation of chromatin organization proteins ...development of primary sexual characteristics / PRC1 complex / 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 / heterochromatin / SUMOylation of DNA damage response and repair proteins / methylated histone binding / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / euchromatin / chromatin organization / Oxidative Stress Induced Senescence / cell differentiation / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Chromobox protein homolog 2 / 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 ...Chromobox protein homolog 2 / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 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 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Derived calculations
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Feb 24, 2016Group: Database references
Revision 2.0Nov 27, 2019Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp / 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 / _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 2
B: unc3866


Theoretical massNumber of molelcules
Total (without water)7,36410
Polymers7,3642
Non-polymers08
Water72140
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-6 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.894, 78.894, 30.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-224-

HOH

31A-225-

HOH

41A-233-

HOH

DetailsAUTHORS HAVE NOT INDICATED THE BIOLOGICAL UNIT

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Components

#1: Protein Chromobox protein homolog 2


Mass: 6568.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q14781
#2: Protein/peptide unc3866


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


Num. of mol.: 8 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.9 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34.16 Å / Num. obs: 10262 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 29.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementResolution: 1.8→34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.69 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 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 ...Details: 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 ESTABLISH PLANAR GEOMETRY OF METHYL ESTER TERMINUS OF INHIBITOR. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY. ELECTRON DENSITY DOES NOT FULLY RESOLVE THE LIGAND'S N-EPSILON ETHYLATION AND C-TERMINAL SERINE METHYL ESTER MOIETY.
RfactorNum. reflection% reflection
Rfree0.212 506 4.9 %
Rwork0.189 --
obs0.19 9752 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms501 0 8 40 549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019535
X-RAY DIFFRACTIONr_bond_other_d0.0030.02528
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.969727
X-RAY DIFFRACTIONr_angle_other_deg1.00931203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.03222.524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3971590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.253155
X-RAY DIFFRACTIONr_chiral_restr0.1130.275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02134
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_it1.7431.723246
X-RAY DIFFRACTIONr_mcbond_other1.6851.632239
X-RAY DIFFRACTIONr_mcangle_it2.4672.557306
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 42 -
Rwork0.223 705 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -25.0186 Å / Origin y: 26.6098 Å / Origin z: -12.1938 Å
111213212223313233
T0.0157 Å2-0.011 Å2-0.0082 Å2-0.0635 Å20.0288 Å2--0.0563 Å2
L6.8523 °22.3198 °21.7025 °2-5.1492 °21.362 °2--4.6661 °2
S0.1503 Å °-0.0974 Å °-0.5091 Å °0.0273 Å °-0.1258 Å °-0.4032 Å °0.1712 Å °0.2224 Å °-0.0245 Å °

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