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- PDB-4hcz: PHF1 Tudor in complex with H3K36me3 -

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Basic information

Entry
Database: PDB / ID: 4hcz
TitlePHF1 Tudor in complex with H3K36me3
Components
  • H3L-like histone
  • PHD finger protein 1
KeywordsTRANSCRIPTION / Protein-peptide complex / Tudor / Histone binding / H3K36me3 / NA / Nucleus
Function / homology
Function and homology information


histone methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / nucleosome / site of double-strand break / chromatin organization / protein heterodimerization activity / centrosome ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / nucleosome / site of double-strand break / chromatin organization / protein heterodimerization activity / centrosome / chromatin binding / regulation of DNA-templated transcription / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
: / : / PHD finger protein 1 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 ...: / : / PHD finger protein 1 / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / 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 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
PHD finger protein 1 / H3L-like histone
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsMusselman, C.A. / Roy, S. / Nunez, J. / Kutateladze, T.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.
Authors: Musselman, C.A. / Avvakumov, N. / Watanabe, R. / Abraham, C.G. / Lalonde, M.E. / Hong, Z. / Allen, C. / Roy, S. / Nunez, J.K. / Nickoloff, J. / Kulesza, C.A. / Yasui, A. / Cote, J. / Kutateladze, T.G.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 1
B: PHD finger protein 1
C: H3L-like histone
D: H3L-like histone


Theoretical massNumber of molelcules
Total (without water)15,4724
Polymers15,4724
Non-polymers00
Water2,900161
1
A: PHD finger protein 1
C: H3L-like histone


Theoretical massNumber of molelcules
Total (without water)7,7362
Polymers7,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area4920 Å2
MethodPISA
2
B: PHD finger protein 1
D: H3L-like histone


Theoretical massNumber of molelcules
Total (without water)7,7362
Polymers7,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area4540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.030, 29.670, 62.000
Angle α, β, γ (deg.)90.000, 116.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHD finger protein 1 / / Protein PHF1 / Polycomb-like protein 1 / hPCl1


Mass: 6623.570 Da / Num. of mol.: 2 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1, PCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43189
#2: Protein/peptide H3L-like histone


Mass: 1112.326 Da / Num. of mol.: 2 / Fragment: H3K36me3 / Source method: obtained synthetically / Details: Synthetic human H3K36me3 peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6TXQ4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 20, 2011
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.85→23.413 Å / Num. all: 12091 / Num. obs: 12091 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.16 Å2
Reflection shellResolution: 1.85→1.92 Å / % possible all: 81.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E5P

2e5p


Resolution: 1.85→23.413 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7729 / SU ML: 0.3 / σ(F): 0 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 580 4.8 %Random
Rwork0.2038 ---
obs0.2058 12073 96.23 %-
all-12091 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.867 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 83.09 Å2 / Biso mean: 30.1275 Å2 / Biso min: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1--3.3304 Å2-0 Å2-1.231 Å2
2---5.0827 Å2-0 Å2
3---8.413 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 161 1222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071085
X-RAY DIFFRACTIONf_angle_d1.061473
X-RAY DIFFRACTIONf_chiral_restr0.071161
X-RAY DIFFRACTIONf_plane_restr0.004183
X-RAY DIFFRACTIONf_dihedral_angle_d14.919409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-2.03610.39321440.28982667281191
2.0361-2.33050.25111560.20612932308899
2.3305-2.93530.27051290.20312977310699
2.9353-23.41440.20661510.18862917306895
Refinement TLS params.Method: refined / Origin x: -0.3947 Å / Origin y: -1.4904 Å / Origin z: 24.6741 Å
111213212223313233
T0.169 Å20.0084 Å20.0061 Å2-0.1649 Å20.0177 Å2--0.1609 Å2
L1.2675 °20.2667 °20.6046 °2-1.3977 °20.8212 °2--0.6479 °2
S-0.0042 Å °0.0173 Å °0.1757 Å °-0.0297 Å °0.0397 Å °0.1476 Å °-0.0169 Å °-0.0492 Å °-0 Å °
Refinement TLS groupSelection details: Chain A

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