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- PDB-8jzw: Cystal structure of HP1 in complex with TRIM66 peptide -

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Basic information

Entry
Database: PDB / ID: 8jzw
TitleCystal structure of HP1 in complex with TRIM66 peptide
Components
  • ASN-SER-GLU-HIS-LYS-ILE-PRO-TYR-VAL-ARG-LEU-GLU-ARG-LEU-LYS-ILE-CYS-ALA
  • Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
KeywordsPROTEIN BINDING / TRIM66 / HP1
Function / homology
Function and homology information


pericentric heterochromatin / methylated histone binding / chromatin organization / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Chromobox protein homologue 3 / 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. ...Chromobox protein homologue 3 / 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. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShen, S.Y. / Li, F.D. / Shi, Y.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Cystal structure of HP1 in complex with TRIM66 peptide
Authors: Shen, S.Y. / Li, F.D. / Shi, Y.Y.
History
DepositionJul 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
D: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
F: ASN-SER-GLU-HIS-LYS-ILE-PRO-TYR-VAL-ARG-LEU-GLU-ARG-LEU-LYS-ILE-CYS-ALA
A: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
B: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
E: ASN-SER-GLU-HIS-LYS-ILE-PRO-TYR-VAL-ARG-LEU-GLU-ARG-LEU-LYS-ILE-CYS-ALA


Theoretical massNumber of molelcules
Total (without water)41,0916
Polymers41,0916
Non-polymers00
Water4,053225
1
C: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
D: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
F: ASN-SER-GLU-HIS-LYS-ILE-PRO-TYR-VAL-ARG-LEU-GLU-ARG-LEU-LYS-ILE-CYS-ALA


Theoretical massNumber of molelcules
Total (without water)20,5453
Polymers20,5453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-24 kcal/mol
Surface area7700 Å2
MethodPISA
2
A: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
B: Chromobox homolog 3 (HP1 gamma homolog, Drosophila)
E: ASN-SER-GLU-HIS-LYS-ILE-PRO-TYR-VAL-ARG-LEU-GLU-ARG-LEU-LYS-ILE-CYS-ALA


Theoretical massNumber of molelcules
Total (without water)20,5453
Polymers20,5453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-23 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.247, 98.690, 40.741
Angle α, β, γ (deg.)90.00, 97.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chromobox homolog 3 (HP1 gamma homolog, Drosophila) / Chromobox homolog 3 (HP1 gamma homolog / Drosophila) / isoform CRA_a / Coiled-coil domain ...Chromobox homolog 3 (HP1 gamma homolog / Drosophila) / isoform CRA_a / Coiled-coil domain containing 32 / isoform CRA_c


Mass: 9185.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3, CCDC32, hCG_1745364, hCG_1999239, tcag7.173 / Production host: Escherichia coli (E. coli) / References: UniProt: A4D177
#2: Protein/peptide ASN-SER-GLU-HIS-LYS-ILE-PRO-TYR-VAL-ARG-LEU-GLU-ARG-LEU-LYS-ILE-CYS-ALA


Mass: 2174.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.76 Å3/Da / Density % sol: 30.05 %
Crystal growTemperature: 293.15 K / Method: batch mode
Details: 30% PEG MME 2000, 0.1 mmol/L sodium cacodylate (pH 6.0)

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2017
Diffraction measurementDetails: 1.00 degrees, 0.1 sec, detector distance 200.00 mm / Method: \w scans
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionAv R equivalents: 0.091 / Number: 176397
ReflectionResolution: 1.8→40 Å / Num. obs: 25428 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/av σ(I): 15.545 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.188 / Num. unique obs: 2491 / Rsym value: 0.576 / % possible all: 94.9
Cell measurementReflection used: 176397

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.94 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1223 4.82 %
Rwork0.1899 --
obs0.1916 25361 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 0 225 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072187
X-RAY DIFFRACTIONf_angle_d0.9052952
X-RAY DIFFRACTIONf_dihedral_angle_d6.164292
X-RAY DIFFRACTIONf_chiral_restr0.055323
X-RAY DIFFRACTIONf_plane_restr0.006376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.27931380.21892616X-RAY DIFFRACTION94
1.87-1.960.28241330.2212653X-RAY DIFFRACTION96
1.96-2.060.2621470.20132668X-RAY DIFFRACTION96
2.06-2.190.24361210.19272693X-RAY DIFFRACTION97
2.19-2.360.22431400.18792657X-RAY DIFFRACTION96
2.36-2.60.23771370.20652693X-RAY DIFFRACTION97
2.6-2.970.26411190.20492709X-RAY DIFFRACTION97
2.97-3.740.21321390.17952704X-RAY DIFFRACTION97
3.74-35.940.18081490.16982745X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 35.4826 Å / Origin y: 25.5392 Å / Origin z: 34.1389 Å
111213212223313233
T0.0701 Å2-0.0229 Å20.0325 Å2-0.1117 Å2-0.001 Å2--0.105 Å2
L0.5227 °2-0.3028 °20.6992 °2-0.7632 °2-0.2287 °2--1.1272 °2
S-0.0035 Å °0.036 Å °-0.0136 Å °0.0388 Å °-0.0068 Å °-0.0599 Å °-0.0148 Å °0.0388 Å °-0.0008 Å °
Refinement TLS groupSelection details: all

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