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- PDB-2fmm: Crystal Structure of EMSY-HP1 complex -

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Basic information

Entry
Database: PDB / ID: 2fmm
TitleCrystal Structure of EMSY-HP1 complex
Components
  • Chromobox protein homolog 1
  • Protein EMSY
KeywordsTRANSCRIPTION / ENT DOMAIN / CHROMO SHADOW DOMAIN / EMSY PROTEIN / HETEROCHROMATIN PROTEIN 1
Function / homology
Function and homology information


chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / methylated histone binding / spindle ...chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / methylated histone binding / spindle / HCMV Early Events / chromatin organization / chromosome, telomeric region / molecular adaptor activity / nuclear body / DNA repair / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
ENT domain / ENT domain / BRCA2-interacting transcriptional repressor EMSY / ENT domain / EMSY N-terminal (ENT) domain profile. / ENT / ENT domain-like superfamily / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain ...ENT domain / ENT domain / BRCA2-interacting transcriptional repressor EMSY / ENT domain / EMSY N-terminal (ENT) domain profile. / ENT / ENT domain-like superfamily / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chromobox protein homolog 1 / BRCA2-interacting transcriptional repressor EMSY
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHuang, Y.
CitationJournal: Structure / Year: 2006
Title: Crystal structure of the HP1-EMSY complex reveals an unusual mode of HP1 binding.
Authors: Huang, Y. / Myers, M.P. / Xu, R.M.
History
DepositionJan 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Protein EMSY
A: Chromobox protein homolog 1
B: Chromobox protein homolog 1
C: Chromobox protein homolog 1
D: Chromobox protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4569
Polymers48,0725
Non-polymers3844
Water6,954386
1
E: Protein EMSY
A: Chromobox protein homolog 1
B: Chromobox protein homolog 1
C: Chromobox protein homolog 1
D: Chromobox protein homolog 1
hetero molecules

E: Protein EMSY
A: Chromobox protein homolog 1
B: Chromobox protein homolog 1
C: Chromobox protein homolog 1
D: Chromobox protein homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,91318
Polymers96,14410
Non-polymers7698
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area25860 Å2
ΔGint-289 kcal/mol
Surface area36500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.400, 63.870, 66.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer of the hetero-pentamer in the asymmetric unit by the operation: 1-x, 1-y, z

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Components

#1: Protein Protein EMSY


Mass: 14530.567 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMSY, C11orf30 / Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z589
#2: Protein
Chromobox protein homolog 1 / Heterochromatin protein 1 homolog beta / HP1 beta / Modifier 1 protein / M31 / Heterochromatin ...Heterochromatin protein 1 homolog beta / HP1 beta / Modifier 1 protein / M31 / Heterochromatin protein p25 / HP1Hsbeta / p25beta


Mass: 8385.410 Da / Num. of mol.: 4 / Fragment: CHROMO SHADOW DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX1, CBX / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P83916
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8M ammonium sulfate, 0.1M tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.97860, 0.97910, 0.96500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97911
30.9651
ReflectionResolution: 1.8→50 Å / Num. all: 57548 / Num. obs: 54308 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.22 / Num. unique all: 55874 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å
RfactorNum. reflection% reflection
Rfree0.243 4421 -
Rwork0.219 --
all0.219 57548 -
obs0.219 54308 94.4 %
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 20 386 3460

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