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- PDB-3q6s: The crystal structure of the heterochromatin protein 1 beta chrom... -

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Basic information

Entry
Database: PDB / ID: 3q6s
TitleThe crystal structure of the heterochromatin protein 1 beta chromoshadow domain complexed with a peptide from Shugoshin 1
Components
  • Chromobox protein homolog 1
  • Shugoshin-like 1
KeywordsCELL CYCLE / INCENP / heterochromatin / centromere
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / centriole-centriole cohesion / meiotic chromosome segregation / chromocenter / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion / histone methyltransferase binding / condensed chromosome, centromeric region / male pronucleus / female pronucleus ...mitotic sister chromatid cohesion, centromeric / centriole-centriole cohesion / meiotic chromosome segregation / chromocenter / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion / histone methyltransferase binding / condensed chromosome, centromeric region / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / methylated histone binding / chromosome segregation / RHO GTPases Activate Formins / spindle / kinetochore / kinase binding / spindle pole / HCMV Early Events / Separation of Sister Chromatids / chromatin organization / chromosome, telomeric region / molecular adaptor activity / nuclear body / cell division / intracellular membrane-bounded organelle / centrosome / DNA damage response / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site ...Shugoshin, C-terminal / Shugoshin, N-terminal coiled-coil domain / Shugoshin / Shugoshin C terminus / Shugoshin N-terminal coiled-coil region / 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
Chromobox protein homolog 1 / Shugoshin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBrautigam, C.A. / Chaudhary, J. / Yu, H.
CitationJournal: Mol Biol Cell / Year: 2011
Title: Mitotic centromeric targeting of HP1 and its binding to Sgo1 are dispensable for sister-chromatid cohesion in human cells.
Authors: Kang, J. / Chaudhary, J. / Dong, H. / Kim, S. / Brautigam, C.A. / Yu, H.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 1
B: Chromobox protein homolog 1
C: Chromobox protein homolog 1
D: Chromobox protein homolog 1
E: Shugoshin-like 1
F: Shugoshin-like 1


Theoretical massNumber of molelcules
Total (without water)40,2416
Polymers40,2416
Non-polymers00
Water2,846158
1
A: Chromobox protein homolog 1
D: Chromobox protein homolog 1
F: Shugoshin-like 1


Theoretical massNumber of molelcules
Total (without water)20,1213
Polymers20,1213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-25 kcal/mol
Surface area8580 Å2
MethodPISA
2
B: Chromobox protein homolog 1
C: Chromobox protein homolog 1
E: Shugoshin-like 1


Theoretical massNumber of molelcules
Total (without water)20,1213
Polymers20,1213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-24 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.816, 108.893, 41.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-3-

HOH

21D-67-

HOH

31D-187-

HOH

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Components

#1: Protein
Chromobox protein homolog 1 / HP1Hsbeta / Heterochromatin protein 1 homolog beta / HP1 beta / Heterochromatin protein p25 / M31 / ...HP1Hsbeta / Heterochromatin protein 1 homolog beta / HP1 beta / Heterochromatin protein p25 / M31 / Modifier 1 protein / p25beta


Mass: 8972.989 Da / Num. of mol.: 4 / Fragment: chromoshadow domain, residues 108-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX1, CBX / Production host: Escherichia coli (E. coli) / References: UniProt: P83916
#2: Protein/peptide Shugoshin-like 1 / hSgo1 / Serologically defined breast cancer antigen NY-BR-85


Mass: 2174.629 Da / Num. of mol.: 2 / Fragment: residues 445-463 / Source method: obtained synthetically / Details: chemically synthesized peptide / References: UniProt: Q5FBB7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.6
Details: 0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789112 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789112 Å / Relative weight: 1
ReflectionResolution: 1.93→62.8 Å / Num. all: 26940 / Num. obs: 26940 / % possible obs: 99.9 % / Observed criterion σ(I): -1000
Reflection shellResolution: 1.93→1.96 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→38.408 Å / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1321 5.08 %random
Rwork0.1902 ---
obs0.1922 26029 95.47 %-
all-26940 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.41 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5051 Å2-0 Å2-0 Å2
2---0.9485 Å20 Å2
3----1.5565 Å2
Refinement stepCycle: LAST / Resolution: 1.93→38.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 158 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122438
X-RAY DIFFRACTIONf_angle_d1.3183306
X-RAY DIFFRACTIONf_dihedral_angle_d12.755916
X-RAY DIFFRACTIONf_chiral_restr0.096354
X-RAY DIFFRACTIONf_plane_restr0.007426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9291-2.00640.30271000.21532198X-RAY DIFFRACTION77
2.0064-2.09770.2451360.2082617X-RAY DIFFRACTION92
2.0977-2.20830.24551440.19722715X-RAY DIFFRACTION96
2.2083-2.34660.23731410.18582764X-RAY DIFFRACTION97
2.3466-2.52770.25611680.19742763X-RAY DIFFRACTION98
2.5277-2.7820.2831590.20912839X-RAY DIFFRACTION99
2.782-3.18440.21991720.20042844X-RAY DIFFRACTION100
3.1844-4.01140.21321550.17252915X-RAY DIFFRACTION100
4.0114-38.41560.20171460.18593053X-RAY DIFFRACTION99
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)
10.6168-0.0798-0.54392.08680.79891.5573-0.0501-0.0230.0663-0.26620.1356-0.305-0.0483-0.1543-0.07730.08860.01330.01920.089-0.0230.11083.417913.137715.831
20.51420.11920.16830.21410.1280.2712-0.05260.03-0.12880.07410.00340.04920.0455-0.02580.03640.1619-0.0598-0.00520.15660.01310.186323.589622.191333.1886
30.4426-0.32470.39720.8106-0.03540.4364-0.053-0.0441-0.02470.0159-0.06330.2166-0.0696-0.0650.09790.0743-0.01020.00540.1367-0.05770.27128.540431.384724.7845
41.10690.0911-0.73981.0583-0.81761.0334-0.2607-0.41060.16620.44870.42510.0309-0.08660.1572-0.02760.17620.13440.07070.08210.183-0.0758-9.274810.531129.9087
50.7031-0.8360.56921.038-0.60030.9374-0.0715-0.02570.0584-0.04890.1796-0.22880.0854-0.0887-0.08730.1754-0.01470.00340.2038-0.05360.362217.823120.022417.1927
61.92441.7297-2.49054.0506-3.08393.84240.0583-0.26710.10660.3245-0.0657-0.1084-0.14130.2869-0.01720.14030.01580.00360.1314-0.01570.1252-6.338225.20322.4307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D
5X-RAY DIFFRACTION5Chain E
6X-RAY DIFFRACTION6Chain F

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