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- PDB-4x3s: Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170... -

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Basic information

Entry
Database: PDB / ID: 4x3s
TitleCrystal structure of chromobox homology 7 (CBX7) with SETDB1-1170me3 Peptide
Components
  • Chromobox protein homolog 7
  • SETDB1-1170me3 Peptide
KeywordsTRANSCRIPTION / CBX7 / chromodomain
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / sebaceous gland development / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / PRC1 complex / transposable element silencing by heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K9me2/3 reader activity ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / sebaceous gland development / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / PRC1 complex / transposable element silencing by heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K9me2/3 reader activity / PcG protein complex / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / PKMTs methylate histone lysines / chromatin organization / chromosome / methylation / single-stranded RNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Chromobox protein homolog 7 / Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / CBX family C-terminal motif / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / CBX family C-terminal motif / Histone methyltransferase Tudor domain ...Chromobox protein homolog 7 / Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / CBX family C-terminal motif / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / CBX family C-terminal motif / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : / Chromo domain subgroup / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Tudor domain / Tudor domain / Post-SET domain / Post-SET domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / Chromo-like domain superfamily / DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / : / Histone-lysine N-methyltransferase SETDB1 / Chromobox protein homolog 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRen, C. / Plotnikov, A.N. / Zhou, M.M.
CitationJournal: Chem.Biol. / Year: 2015
Title: Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain.
Authors: Ren, C. / Morohashi, K. / Plotnikov, A.N. / Jakoncic, J. / Smith, S.G. / Li, J. / Zeng, L. / Rodriguez, Y. / Stojanoff, V. / Walsh, M. / Zhou, M.M.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 7
B: Chromobox protein homolog 7
C: SETDB1-1170me3 Peptide
D: SETDB1-1170me3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,57910
Polymers17,6984
Non-polymers8806
Water3,405189
1
A: Chromobox protein homolog 7
D: SETDB1-1170me3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2895
Polymers8,8492
Non-polymers4403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-24 kcal/mol
Surface area5540 Å2
MethodPISA
2
B: Chromobox protein homolog 7
C: SETDB1-1170me3 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2895
Polymers8,8492
Non-polymers4403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-24 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.027, 46.040, 80.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromobox protein homolog 7


Mass: 7730.877 Da / Num. of mol.: 2 / Fragment: UNP residues 7-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbx7, D15Ertd417e / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VDS3
#2: Protein/peptide SETDB1-1170me3 Peptide


Mass: 1118.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15047*PLUS
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% Jeffamine M-600, 0.1 M Na Citrate pH 5.6, 0.01 M FeCl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40.4 Å / Num. obs: 23204 / % possible obs: 99.36 % / Redundancy: 4.6 % / Net I/σ(I): 42.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I91

3i91


Resolution: 1.6→23.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.606 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22154 1195 5.1 %RANDOM
Rwork0.1621 ---
obs0.16506 22009 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.087 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.1 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 54 189 1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191281
X-RAY DIFFRACTIONr_bond_other_d0.0010.021231
X-RAY DIFFRACTIONr_angle_refined_deg1.7372.0081725
X-RAY DIFFRACTIONr_angle_other_deg0.81832839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.64521.61362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1215232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6451516
X-RAY DIFFRACTIONr_chiral_restr0.1160.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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_restr7.44832512
X-RAY DIFFRACTIONr_sphericity_free24.363548
X-RAY DIFFRACTIONr_sphericity_bonded13.15752629
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 91 -
Rwork0.256 1567 -
obs--99.1 %

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