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- PDB-1pfb: Structural Basis for specific binding of polycomb chromodomain to... -

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Basic information

Entry
Database: PDB / ID: 1pfb
TitleStructural Basis for specific binding of polycomb chromodomain to histone H3 methylated at K27
Components
  • Histone H3, embryonic
  • Polycomb protein
KeywordsPEPTIDE BINDING PROTEIN / chromatin / histone methylation / polycomb / chromodomain
Function / homology
Function and homology information


negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / ventral cord development ...negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / ventral cord development / Oxidative Stress Induced Senescence / PRC1 complex / polytene chromosome / anterior/posterior axis specification / neuron remodeling / : / neurogenesis / wound healing / structural constituent of chromatin / nucleosome / heterochromatin formation / sequence-specific DNA binding / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
: / CBX family C-terminal motif / CBX family C-terminal motif / 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 ...: / CBX family C-terminal motif / CBX family C-terminal motif / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / BETA-MERCAPTOETHANOL / Histone H3, embryonic / Polycomb group protein Pc
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMin, J.R. / Zhang, Y. / Xu, R.-M.
CitationJournal: Genes Dev. / Year: 2003
Title: Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27.
Authors: Min, J.R. / Zhang, Y. / Xu, R.-M.
History
DepositionMay 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein
B: Histone H3, embryonic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1746
Polymers7,9652
Non-polymers2094
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area4880 Å2
MethodPISA
2
A: Polycomb protein
B: Histone H3, embryonic
hetero molecules

A: Polycomb protein
B: Histone H3, embryonic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,34912
Polymers15,9304
Non-polymers4188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area4300 Å2
ΔGint-36 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.429, 77.033, 77.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-204-

CL

31A-205-

HOH

41A-332-

HOH

51A-339-

HOH

61A-340-

HOH

71A-341-

HOH

81B-2-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Polycomb protein


Mass: 6806.826 Da / Num. of mol.: 1 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PC OR CG7618 / Production host: Escherichia coli (E. coli) / References: UniProt: P26017
#2: Protein/peptide Histone H3, embryonic


Mass: 1158.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is naturally found in Strongylocentrotus purpuratus.
References: UniProt: P06352

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG8000, 200mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
25 %Tris1droppH8.0
3200 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
6100 mMsodium cacodylate1reservoirpH6.5
70.2 Mammonium sulfate1reservoir
830 %PEG80001reservoir
910 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 19520 / Num. obs: 17050 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å / % possible all: 42.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 85538 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 42.3 % / Num. unique obs: 811 / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→27.28 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.216 1701 random
Rwork0.197 --
all-17050 -
obs-17050 -
Refinement stepCycle: LAST / Resolution: 1.4→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms559 0 6 151 716
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.29
X-RAY DIFFRACTIONdihedral_angle_d
X-RAY DIFFRACTIONdihedral_angle_deg24.12
X-RAY DIFFRACTIONimproper_angle_d
X-RAY DIFFRACTIONimproper_angle_deg0.7
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.46 Å / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.298

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