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- PDB-5epl: Crystal Structure of chromodomain of CBX4 in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 5epl
TitleCrystal Structure of chromodomain of CBX4 in complex with inhibitor UNC3866
Components
  • E3 SUMO-protein ligase CBX4
  • unc3866
Keywordstranscription/transcription inhibitor / structural genomics / Structural Genomics Consortium / SGC / transcription-transcription inhibitor complex
Function / homology
Function and homology information


PRC1 complex / SUMO ligase activity / PcG protein complex / SUMO binding / SUMOylation of DNA methylation proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / SUMO transferase activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / protein sumoylation ...PRC1 complex / SUMO ligase activity / PcG protein complex / SUMO binding / SUMOylation of DNA methylation proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / SUMO transferase activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / protein sumoylation / 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 / phosphoprotein binding / transcription corepressor activity / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / nuclear body / transcription cis-regulatory region binding / nuclear speck / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
E3 SUMO-protein ligase CBX4 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / 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 ...E3 SUMO-protein ligase CBX4 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / 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 / E3 SUMO-protein ligase CBX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 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: Structure summary
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Feb 24, 2016Group: Database references
Revision 2.0Nov 27, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _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: E3 SUMO-protein ligase CBX4
B: E3 SUMO-protein ligase CBX4
C: unc3866
D: unc3866


Theoretical massNumber of molelcules
Total (without water)16,29912
Polymers16,2994
Non-polymers08
Water2,108117
1
A: E3 SUMO-protein ligase CBX4
C: unc3866


Theoretical massNumber of molelcules
Total (without water)8,1495
Polymers8,1492
Non-polymers03
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area4320 Å2
MethodPISA
2
B: E3 SUMO-protein ligase CBX4
D: unc3866


Theoretical massNumber of molelcules
Total (without water)8,1497
Polymers8,1492
Non-polymers05
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-6 kcal/mol
Surface area4490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.178, 65.178, 133.057
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsAUTHORS HAVE NOT INDICATED THE BIOLOGICAL UNIT

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Components

#1: Protein E3 SUMO-protein ligase CBX4 / Chromobox protein homolog 4 / Polycomb 2 homolog / hPc2


Mass: 7354.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX4 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: O00257, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide unc3866


Type: Oligopeptide / Class: Inhibitor / Mass: 795.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / 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.: 117 / 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: 2.7 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% PEG3350, 0.2M sodium chloride, 0.1 M sodium cacodylate

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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: 1.81→44.35 Å / Num. obs: 16048 / % possible obs: 99.9 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 37.4
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 5.4 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementResolution: 1.81→44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.79 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH AN ISOMORPHOUS CRYSTAL, FOLLOWED BY PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING WITH ARP/WARP. PHENIX.ELBOW/MOGUL WAS USED TO ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH AN ISOMORPHOUS CRYSTAL, FOLLOWED BY PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING WITH ARP/WARP. PHENIX.ELBOW/MOGUL WAS USED TO GENERATE GEOMETRY RESTRAINTS FOR INHIBITOR BUILDING BLOCKS. LIGAND 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 DID NOT FULLY RESOLVE THE LIGAND'S C-TERMINAL SERINE ESTER MOIETY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1566 9.8 %THIN SHELLS (SFTOOLS)
Rwork0.183 ---
obs0.187 14370 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.81→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 8 117 1165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191102
X-RAY DIFFRACTIONr_bond_other_d0.0020.021071
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9531499
X-RAY DIFFRACTIONr_angle_other_deg1.03732449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.32922.30852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82615182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5521511
X-RAY DIFFRACTIONr_chiral_restr0.1110.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02268
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_it1.6921.777500
X-RAY DIFFRACTIONr_mcbond_other1.6711.757493
X-RAY DIFFRACTIONr_mcangle_it2.4282.645622
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: 1.81→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.197 1142 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.24460.3394-0.28631.15280.81253.56250.01830.0351-0.0757-0.11530.0238-0.1379-0.09560.1602-0.04220.0269-0.00390.00220.00910.00070.0259-17.61444.38275.4479
23.91042.402-0.68345.065-0.41042.44530.0178-0.2141-0.2270.2322-0.1629-0.03050.1298-0.16980.14510.023-0.00810.0090.0546-0.00750.0251-38.726433.67928.9303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 59
2X-RAY DIFFRACTION2B6 - 63

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