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- PDB-5t1g: chromo shadow domain of CBX1 in complex with a histone peptide -

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Basic information

Entry
Database: PDB / ID: 5t1g
Titlechromo shadow domain of CBX1 in complex with a histone peptide
Components
  • Chromobox protein homolog 1
  • Histone H3.1
KeywordsTRANSCRIPTION / chromo shadow domain / structural genomics consortium / SGC
Function / homology
Function and homology information


chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / epigenetic regulation of gene expression ...chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear body / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Chromobox protein homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: chromo shadow domain of CBX1 in complex with a histone peptide
Authors: Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 1
B: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)10,89710
Polymers10,8972
Non-polymers08
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-3 kcal/mol
Surface area4280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.657, 76.887, 78.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
SymmetryPoint symmetry: (Schoenflies symbol: I2 (icosahedral))
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

DetailsAuthors are unsure about the biological significance of the interaction observed in the asymmetric unit. CSD dimer has been assigned as for the PDB entry 1DZ1

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Components

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


Mass: 9030.041 Da / Num. of mol.: 1 / Fragment: unp residues 108-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX1, CBX / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P83916
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c


Mass: 1867.186 Da / Num. of mol.: 1 / Fragment: unp residues 39-53 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#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.: 15 / 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: 43.99 % / Mosaicity: 0.16 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5 M sodium citrate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791827 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791827 Å / Relative weight: 1
ReflectionResolution: 1.8→43.07 Å / Num. obs: 9891 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.081 / Net I/σ(I): 16.9 / Num. measured all: 71509
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.846.91.4781.339055640.7880.5961.59699.4
9-43.075.60.02856.9525940.9970.0130.03197

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FMM

2fmm


Resolution: 1.9→43.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.841 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Some C-terminal residues of the CBX1 construct were not observed in the crysal structure. Electron density currently assigned to the histone peptide may instead have arisen from unobserved ...Details: Some C-terminal residues of the CBX1 construct were not observed in the crysal structure. Electron density currently assigned to the histone peptide may instead have arisen from unobserved CBX1 residues. The course of the peptide main chain at the position of histone Arg-49 remains uncertain. In an alternative interpretation of the crystal packing, the histone peptide interacts with histone residues 142..146.
RfactorNum. reflection% reflection
Rfree0.2431 839 9.9 %
Rwork0.2126 --
obs0.2156 7611 99.88 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.81 Å2 / Biso mean: 34.927 Å2 / Biso min: 20.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å20 Å2
2--3.28 Å2-0 Å2
3----3.71 Å2
Refinement stepCycle: final / Resolution: 1.9→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms487 0 8 15 510
Biso mean--33.19 37.86 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019521
X-RAY DIFFRACTIONr_bond_other_d0.0020.02485
X-RAY DIFFRACTIONr_angle_refined_deg1.481.973711
X-RAY DIFFRACTIONr_angle_other_deg0.93131118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.847572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49824.76221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7351582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.403153
X-RAY DIFFRACTIONr_chiral_restr0.090.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021613
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02110
X-RAY DIFFRACTIONr_mcbond_it1.2752.53277
X-RAY DIFFRACTIONr_mcbond_other1.2752.538278
X-RAY DIFFRACTIONr_mcangle_it2.0653.77348
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 57 -
Rwork0.295 556 -
all-613 -
obs--99.84 %
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)
16.90320.01361.63871.5155-0.75295.8659-0.1158-0.1202-0.05860.16480.10510.03640.2043-0.43870.01070.0433-0.00280.01080.04610.00530.00436.0036-22.7278-8.9324
211.40835.7863-3.079217.5787-5.61774.15340.1142-0.0376-0.0002-0.036-0.14950.2016-0.01240.32920.03530.13180.02270.00580.1412-0.04390.07655.2198-23.19163.7012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 168
2X-RAY DIFFRACTION2B44 - 50

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