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- PDB-3fdt: Crystal structure of the complex of human chromobox homolog 5 (CB... -

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Basic information

Entry
Database: PDB / ID: 3fdt
TitleCrystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide
Components
  • Chromobox protein homolog 5
  • H3K9(me)3 peptide
KeywordsPROTEIN BINDING / chromobox homolog5 / CBX5 / H3K9(me)3 peptide / Structural Genomics / Structural Genomics Consortium / SGC / Centromere / Nucleus / Phosphoprotein / Chromosomal protein / DNA-binding / Nucleosome core
Function / homology
Function and homology information


chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / ribonucleoprotein complex binding / epigenetic regulation of gene expression ...chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / ribonucleoprotein complex binding / epigenetic regulation of gene expression / methylated histone binding / telomere organization / transcription repressor complex / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / kinetochore / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / histone deacetylase binding / structural constituent of chromatin / nucleosome / protein-macromolecule adaptor activity / nuclear envelope / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / Estrogen-dependent gene expression / chromosome, telomeric region / cadherin binding / ribonucleoprotein complex / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / 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
Chromobox protein homolog 5 / Histone H3.1 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAmaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Ravichandran, M. / 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: J.Biol.Chem. / Year: 2011
Title: Recognition and specificity determinants of the human cbx chromodomains.
Authors: Kaustov, L. / Ouyang, H. / Amaya, M. / Lemak, A. / Nady, N. / Duan, S. / Wasney, G.A. / Li, Z. / Vedadi, M. / Schapira, M. / Min, J. / Arrowsmith, C.H.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 5
T: H3K9(me)3 peptide


Theoretical massNumber of molelcules
Total (without water)8,8132
Polymers8,8132
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-6 kcal/mol
Surface area4330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.123, 73.123, 28.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-75-

HOH

21A-78-

HOH

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Components

#1: Protein Chromobox protein homolog 5 / Heterochromatin protein 1 homolog alpha / HP1 alpha / Antigen p25


Mass: 7205.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX5, HP1A / Production host: Escherichia coli (E. coli) / References: UniProt: P45973
#2: Protein/peptide H3K9(me)3 peptide


Mass: 1607.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q3BDD9, UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG 400, 0.2M Na Cl, 0.1M Tris (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorDate: Nov 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 5592 / % possible obs: 99.6 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.086
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2-2.076.70.38196.9
2.07-2.159.40.336100
2.15-2.2511.40.274100
2.25-2.3712.60.244100
2.37-2.5213.70.19100
2.52-2.7113.90.149100
2.71-2.9913.90.113100
2.99-3.4213.80.084100
3.42-4.3113.20.067100
4.31-10012.10.06799.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F2U

3f2u


Resolution: 2→51.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.651 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25739 253 4.5 %RANDOM
Rwork0.19665 ---
obs0.19928 5310 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms495 0 0 34 529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.968681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.55524.58324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4431587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.139153
X-RAY DIFFRACTIONr_chiral_restr0.1190.275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2196
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2350
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0531.5308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9612484
X-RAY DIFFRACTIONr_scbond_it3.3953224
X-RAY DIFFRACTIONr_scangle_it5.94.5197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 22 -
Rwork0.241 362 -
obs--96 %

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