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- PDB-9c0o: Crystal structure of DmCfp1 PHD finger bound to H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 9c0o
TitleCrystal structure of DmCfp1 PHD finger bound to H3K4me3
Components
  • CXXC-type zinc finger protein 1
  • Histone H3.3C
KeywordsMETAL BINDING PROTEIN / Chromatin binding protein / histone H3 reader
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / Set1C/COMPASS complex / nucleosomal DNA binding / methylated histone binding / euchromatin / structural constituent of chromatin / nucleosome / positive regulation of cell growth / protein heterodimerization activity / positive regulation of DNA-templated transcription ...Formation of WDR5-containing histone-modifying complexes / Set1C/COMPASS complex / nucleosomal DNA binding / methylated histone binding / euchromatin / structural constituent of chromatin / nucleosome / positive regulation of cell growth / protein heterodimerization activity / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
CpG binding protein, C-terminal / CpG binding protein C-terminal domain / Spp1/CFP1 / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...CpG binding protein, C-terminal / CpG binding protein C-terminal domain / Spp1/CFP1 / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.3C / CXXC-type zinc finger protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGregoire, S. / Couture, J.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148533 Canada
Citation
Journal: Structure / Year: 2024
Title: Structural insights into an atypical histone binding mechanism by a PHD finger.
Authors: Gregoire, S. / Gregoire, J. / Yang, Y. / Capitani, S. / Joshi, M. / Sarvan, S. / Zaker, A. / Ning, Z. / Figeys, D. / Ulrich, K. / Brunzelle, J.S. / Mer, A. / Couture, J.F.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 25, 2024Group: Database references / Category: citation / Item: _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CXXC-type zinc finger protein 1
D: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9398
Polymers9,4732
Non-polymers4666
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-82 kcal/mol
Surface area5230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.270, 43.120, 47.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein CXXC-type zinc finger protein 1 / PHD finger and CXXC domain-containing protein 1


Mass: 7772.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Cfp1, CG17446
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9W352
#2: Protein/peptide Histone H3.3C / Histone H3.5


Mass: 1699.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2

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Non-polymers , 4 types, 76 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.8 Å3/Da / Density % sol: 31.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 0.01M Tris pH8.5, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→31.95 Å / Num. obs: 10748 / % possible obs: 99.46 % / Redundancy: 12.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.039 / Rrim(I) all: 0.14 / Χ2: 1 / Net I/σ(I): 11.6
Reflection shellResolution: 1.53→1.585 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.372 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1046 / Rpim(I) all: 0.381 / Rrim(I) all: 1.425 / Χ2: 0.91 / % possible all: 98.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.15data scaling
PHASERphasing
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→31.95 Å / SU ML: 0.1455 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1936 548 5.1 %
Rwork0.1562 10198 -
obs0.158 10746 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.29 Å2
Refinement stepCycle: LAST / Resolution: 1.53→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms582 0 17 70 669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038648
X-RAY DIFFRACTIONf_angle_d0.7132873
X-RAY DIFFRACTIONf_chiral_restr0.049184
X-RAY DIFFRACTIONf_plane_restr0.005115
X-RAY DIFFRACTIONf_dihedral_angle_d6.038894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.680.25181270.17752478X-RAY DIFFRACTION98.9
1.68-1.930.22341410.16072493X-RAY DIFFRACTION99.36
1.93-2.430.21261260.15472567X-RAY DIFFRACTION99.59
2.43-31.950.17161540.15232660X-RAY DIFFRACTION99.96

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