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- PDB-3g7l: Chromodomain of Chp1 in complex with Histone H3K9me3 peptide -

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Basic information

Entry
Database: PDB / ID: 3g7l
TitleChromodomain of Chp1 in complex with Histone H3K9me3 peptide
Components
  • Chromo domain-containing protein 1
  • Histone H3.1/H3.2
KeywordsNUCLEAR PROTEIN / chromodomain / protein-peptide complex / silencing / Cell cycle / Chromosome partition / DNA-binding / Nucleus / RNA-mediated gene silencing / Acetylation / Chromosomal protein / DNA damage / DNA repair / Methylation / Nucleosome core / Phosphoprotein
Function / homology
Function and homology information


nucleolar peripheral inclusion body / RITS complex / siRNA-mediated pericentric heterochromatin formation / mating-type region heterochromatin / heterochromatin island / heterochromatin boundary formation / mitotic sister chromatid biorientation / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / chromatin-protein adaptor activity ...nucleolar peripheral inclusion body / RITS complex / siRNA-mediated pericentric heterochromatin formation / mating-type region heterochromatin / heterochromatin island / heterochromatin boundary formation / mitotic sister chromatid biorientation / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / chromatin-protein adaptor activity / spindle pole body / subtelomeric heterochromatin formation / heterochromatin / pericentric heterochromatin / methylated histone binding / histone reader activity / chromosome segregation / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / single-stranded RNA binding / protein heterodimerization activity / DNA damage response / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
: / Chromo domain-containing protein 1-like, PIN domain / 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 domain-containing protein 1-like, PIN domain / 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 / RNA-binding domain superfamily / 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
ACETIC ACID / Histone H3.1/H3.2 / Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchalch, T. / Joshua-Tor, L.
CitationJournal: Mol.Cell / Year: 2009
Title: High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin
Authors: Schalch, T. / Job, G. / Noffsinger, V.J. / Shanker, S. / Kuscu, C. / Joshua-Tor, L. / Partridge, J.F.
History
DepositionFeb 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromo domain-containing protein 1
P: Histone H3.1/H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4767
Polymers9,1542
Non-polymers3225
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-68 kcal/mol
Surface area4420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.560, 41.560, 87.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Chromo domain-containing protein 1


Mass: 7383.179 Da / Num. of mol.: 1 / Fragment: Chromodomain (UNP residues 15 to 75)
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-Sumo fusion
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: chp1, SPAC18G6.02c / Plasmid: pET28a-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q10103
#2: Protein/peptide Histone H3.1/H3.2


Mass: 1771.051 Da / Num. of mol.: 1 / Fragment: UNP residues 2 to 17 / Mutation: R17Y / Source method: obtained synthetically
Details: Peptide synthesis by Protein Peptide Research Ldt., Hampshire UK.
References: UniProt: P09988
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M Zinc Acetate, 20% w/v PEG 3350, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Feb 9, 2007
RadiationMonochromator: CRYOGENICALLY COOLED DOUBLE CRYSTAL MONOCHROMATOR WITH HORIZONTAL FOCUSING SAGITTAL BEND SECOND MONO CRYSTAL WITH 4:1 MAGNIFICATION RATIO AND VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.2→19.3 Å / Num. all: 7418 / Num. obs: 7255 / % possible obs: 97.93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 44.94 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.87
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.46 / Num. unique all: 1683 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A of pdb code 1KNE

1kne


Resolution: 2.2→19.337 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic and TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CCP4 monomer library
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 713 9.83 %10% of data. selection by phenix.refine
Rwork0.1958 ---
all0.2001 7418 --
obs0.2001 7250 97.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.891 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 4 36 1094
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg0.798
X-RAY DIFFRACTIONf_dihedral_angle_d13.27
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.36990.34971390.28121319X-RAY DIFFRACTION100
2.3699-2.60790.35331460.22351346X-RAY DIFFRACTION100
2.6079-2.98410.23071470.20511322X-RAY DIFFRACTION99
2.9841-3.75510.25431430.15511300X-RAY DIFFRACTION97
3.7551-19.33730.17931380.18071250X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 0.5302 Å / Origin y: -17.8348 Å / Origin z: -9.4336 Å
111213212223313233
T0.1809 Å20.0433 Å20.0361 Å2-0.1886 Å2-0.0261 Å2--0.1274 Å2
L4.4395 °2-0.6834 °2-0.9464 °2-2.1005 °20.2853 °2--0.2208 °2
S0.2489 Å °-0.0296 Å °-0.0223 Å °-0.171 Å °-0.3178 Å °-0.108 Å °-0.3306 Å °0.0213 Å °0.0546 Å °
Refinement TLS groupSelection details: all

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