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- PDB-3f2u: Crystal structure of human chromobox homolog 1 (CBX1) -

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Basic information

Entry
Database: PDB / ID: 3f2u
TitleCrystal structure of human chromobox homolog 1 (CBX1)
ComponentsChromobox protein homolog 1
KeywordsPROTEIN BINDING / Human chromobox homolog 1 / CBX1 / Structural Genomics / Structural Genomics Consortium / SGC / Centromere / Nucleus / Phosphoprotein
Function / homology
Function and homology information


chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / methylated histone binding / HCMV Early Events ...chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / methylated histone binding / HCMV Early Events / spindle / chromatin organization / chromosome, telomeric region / nuclear body / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / 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 shadow domain / Chromo shadow domain / Chromo Shadow Domain / 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
Chromobox protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAmaya, M.F. / Ravichandran, M. / Tempel, W. / Wernimont, A.K. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. ...Amaya, M.F. / Ravichandran, M. / Tempel, W. / Wernimont, A.K. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Botchkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the complex of human chromobox homolog 1 (CBX1)
Authors: Ravichandran, M. / Amaya, M.F. / Tempel, W. / Wernimont, A.K. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Botchkarev, A. / Min, J. / Ouyang, H.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 1


Theoretical massNumber of molelcules
Total (without water)6,4961
Polymers6,4961
Non-polymers00
Water50428
1
A: Chromobox protein homolog 1

A: Chromobox protein homolog 1


Theoretical massNumber of molelcules
Total (without water)12,9932
Polymers12,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area850 Å2
ΔGint-7 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.057, 39.068, 37.832
Angle α, β, γ (deg.)90.000, 137.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromobox protein homolog 1 / Heterochromatin protein 1 homolog beta / HP1 beta / Modifier 1 protein / M31 / Heterochromatin ...Heterochromatin protein 1 homolog beta / HP1 beta / Modifier 1 protein / M31 / Heterochromatin protein p25 / HP1Hsbeta / p25beta


Mass: 6496.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX1, CBX / Production host: Escherichia coli (E. coli) / References: UniProt: P83916
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 0.2M CaCl2 0.1M Na Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 4815 / Num. obs: 4818

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DM1

3dm1


Resolution: 1.8→27.18 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.85 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 219 4.7 %RANDOM
Rwork0.222 ---
obs0.224 4660 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.65 Å2 / Biso mean: 11.545 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å21.78 Å2
2---1.2 Å20 Å2
3---2.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms393 0 0 28 421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022402
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.958547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.397550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.94424.11817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6221562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.996152
X-RAY DIFFRACTIONr_chiral_restr0.1060.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02304
X-RAY DIFFRACTIONr_nbd_refined0.2230.2147
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.224
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3930.28
X-RAY DIFFRACTIONr_mcbond_it0.9621.5260
X-RAY DIFFRACTIONr_mcangle_it1.3462400
X-RAY DIFFRACTIONr_scbond_it2.3143172
X-RAY DIFFRACTIONr_scangle_it3.1114.5147
LS refinement shellResolution: 1.795→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 17 -
Rwork0.194 286 -
all-303 -
obs--87.83 %
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)
12.71970.3614-1.04211.6890.19376.6537-0.155-0.04070.0901-0.1473-0.04520.02690.0014-0.35790.20020.09640.01130.00110.2011-0.04480.042611.1652-5.65254.8411
26.93846.3289-0.16157.3218-2.03742.31020.0571-0.36460.324-0.1036-0.2350.2937-0.0193-0.01350.17790.11780.00490.01240.1787-0.04610.047813.48582.34744.4623
38.52781.5456-4.28666.07471.947420.6783-0.00590.2225-1.14-0.00320.2687-0.301-0.55080.5203-0.26280.0578-0.01860.07970.2014-0.0670.253620.5575-5.57460.9757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION2A11 - 38
3X-RAY DIFFRACTION3A39 - 51

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