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- PDB-3i8z: Crystal structure of human chromobox homolog 4 (CBX4) -

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Basic information

Entry
Database: PDB / ID: 3i8z
TitleCrystal structure of human chromobox homolog 4 (CBX4)
ComponentsE3 SUMO-protein ligase CBX4
KeywordsTRANSCRIPTION / chromobox homolog 4 / CBX4 / Structural Genomics / Structural Genomics Consortium / SGC / Alternative splicing / Chromatin regulator / Isopeptide bond / Nucleus / Phosphoprotein / Repressor / Transcription regulation / Ubl conjugation / Ubl conjugation pathway
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
E3 SUMO-protein ligase CBX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsAmaya, M.F. / Zhihong, L. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Zhihong, L. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human chromobox homolog 4 (CBX4)
Authors: Zhihong, L. / Amaya, M.F. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 SUMO-protein ligase CBX4


Theoretical massNumber of molelcules
Total (without water)6,8251
Polymers6,8251
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.606, 58.606, 32.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein E3 SUMO-protein ligase CBX4 / Chromobox protein homolog 4 / Polycomb 2 homolog / Pc2 / hPc2


Mass: 6824.825 Da / Num. of mol.: 1 / Fragment: Chromo domain: UNP residues 8-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O00257
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% Isopropanol, 20% PEG 4000, 0.1 M Na Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Details: Rh-coated Si mirror for vertical focusing
RadiationMonochromator: Bent triangular asymmetric cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 8902 / % possible obs: 98.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Χ2: 3.677 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.554.60.2247761.66286.8
1.55-1.625.80.1898861.58999.9
1.62-1.697.10.1559151.648100
1.69-1.787.30.1248962.091100
1.78-1.897.40.118942.599100
1.89-2.047.40.0969053.468100
2.04-2.247.40.0849044.065100
2.24-2.567.40.0758964.093100
2.56-3.237.40.0649144.059100
3.23-406.90.08591610.19697.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H91

3h91


Resolution: 1.51→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.375 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 425 4.8 %RANDOM
Rwork0.228 ---
obs0.229 8902 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.76 Å2 / Biso mean: 21.568 Å2 / Biso min: 10.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.51→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms437 0 0 59 496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022449
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.944605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.123549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43322.08324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4161585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.367156
X-RAY DIFFRACTIONr_chiral_restr0.0890.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02342
X-RAY DIFFRACTIONr_nbd_refined0.2180.2168
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.210
X-RAY DIFFRACTIONr_mcbond_it0.9541.5256
X-RAY DIFFRACTIONr_mcangle_it1.4732406
X-RAY DIFFRACTIONr_scbond_it2.383229
X-RAY DIFFRACTIONr_scangle_it3.9854.5199
LS refinement shellResolution: 1.51→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 31 -
Rwork0.267 622 -
all-653 -
obs--98.94 %

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