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- PDB-3p7j: Drosophila HP1a chromo shadow domain -

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Basic information

Entry
Database: PDB / ID: 3p7j
TitleDrosophila HP1a chromo shadow domain
ComponentsHeterochromatin protein 1
KeywordsTRANSCRIPTION / heterochromatin protein 1 / chromo shadow domain / gene silencing / epigenetics
Function / homology
Function and homology information


protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / satellite DNA binding / : / polytene chromosome / chromocenter / rDNA binding / pericentric heterochromatin formation ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / satellite DNA binding / : / polytene chromosome / chromocenter / rDNA binding / pericentric heterochromatin formation / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / pericentric heterochromatin / heterochromatin / condensed chromosome / Hsp70 protein binding / telomere maintenance / methylated histone binding / euchromatin / heterochromatin formation / mitotic cell cycle / chromosome / protein-macromolecule adaptor activity / histone binding / chromosome, telomeric region / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / 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. ...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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Heterochromatin protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, D. / Chruszcz, M. / Minor, W. / Khorasanizadeh, S.
CitationJournal: Chembiochem / Year: 2011
Title: The HP1a Disordered C Terminus and Chromo Shadow Domain Cooperate to Select Target Peptide Partners.
Authors: Mendez, D.L. / Kim, D. / Chruszcz, M. / Stephens, G.E. / Minor, W. / Khorasanizadeh, S. / Elgin, S.C.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Heterochromatin protein 1
B: Heterochromatin protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1633
Polymers20,0702
Non-polymers921
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterochromatin protein 1
hetero molecules

A: Heterochromatin protein 1


Theoretical massNumber of molelcules
Total (without water)20,1633
Polymers20,0702
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area1640 Å2
ΔGint-9 kcal/mol
Surface area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.755, 56.545, 67.295
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 Heterochromatin protein 1 / HP1 / Non-histone chromosomal protein C1A9 antigen


Mass: 10035.203 Da / Num. of mol.: 2 / Fragment: UNP residues 131-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(var)205, HP1, CG8409 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: P05205
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG400, 0.1 M HEPES. Cryoprotected in 12% PEG400, 0.1 M HEPES, 33% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2009 / Details: mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 8023 / Num. obs: 8023 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 37.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.3 / Num. unique all: 397 / Rsym value: 0.475 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
CNSrefinement
REFMAC5.5.0109refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FMM

2fmm


Resolution: 2.3→31.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.616 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24613 370 4.6 %RANDOM
Rwork0.19853 ---
all0.20094 7607 --
obs0.20094 7607 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.534 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å20 Å2
2---1.03 Å20 Å2
3----2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 6 37 983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0190.022959
X-RAY DIFFRACTIONf_bond_other_d0.0060.02672
X-RAY DIFFRACTIONf_angle_refined_deg1.4211.9691285
X-RAY DIFFRACTIONf_angle_other_deg0.8431630
X-RAY DIFFRACTIONf_dihedral_angle_1_deg5.4845118
X-RAY DIFFRACTIONf_dihedral_angle_2_deg39.50424.16748
X-RAY DIFFRACTIONf_dihedral_angle_3_deg14.67415172
X-RAY DIFFRACTIONf_dihedral_angle_4_deg10.147158
X-RAY DIFFRACTIONf_chiral_restr0.0930.2140
X-RAY DIFFRACTIONf_gen_planes_refined0.0050.021066
X-RAY DIFFRACTIONf_gen_planes_other0.0010.02198
X-RAY DIFFRACTIONf_nbd_refined
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it0.9761.5592
X-RAY DIFFRACTIONf_mcbond_other0.0371.5244
X-RAY DIFFRACTIONf_mcangle_it1.772946
X-RAY DIFFRACTIONf_scbond_it2.4723367
X-RAY DIFFRACTIONf_scangle_it3.944.5339
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 25 -
Rwork0.22 566 -
obs--98.99 %
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)
15.88723.68740.59549.42472.3855.6858-0.02-0.04080.296-0.2263-0.0630.3083-0.2965-0.22220.0830.03080.00970.00240.0313-0.01160.0501-19.0304-5.8247-22.3063
210.2013.2941-8.936810.4483-1.00568.26650.09020.50240.7998-0.40280.20311.2847-0.1333-0.5749-0.29340.1950.0681-0.10860.3208-0.23590.4775-22.64121.6355-16.9052
323.54555.39758.979713.77594.787526.43550.4129-0.5427-1.09660.6645-0.0907-0.79251.57290.9904-0.32220.18430.1129-0.05560.1429-0.01340.1169-14.5889-4.5241-9.0934
47.6506-2.81892.81068.8585-0.35426.5998-0.13-0.30390.08610.5908-0.03890.2525-0.083-0.51340.16890.08750.0070.01470.0556-0.01750.0198-15.70768.19484.4246
54.0514-7.03845.682219.7618-1.688816.91060.0777-0.3518-0.5330.51260.24331.23290.7185-0.9472-0.3210.1082-0.0260.01690.18660.00410.2097-22.09712.8621-1.0251
613.5965-3.24320.020412.8303-0.410114.04510.17270.4550.3303-0.3323-0.3654-1.2388-0.08031.25510.19260.0270.02270.02050.15250.03610.131-12.40816.1165-9.2443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A141 - 178
2X-RAY DIFFRACTION2A179 - 187
3X-RAY DIFFRACTION3A188 - 200
4X-RAY DIFFRACTION4B141 - 178
5X-RAY DIFFRACTION5B179 - 187
6X-RAY DIFFRACTION6B188 - 200

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