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- PDB-2x35: Molecular basis of Histone H3K36me3 recognition by the PWWP domai... -

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Basic information

Entry
Database: PDB / ID: 2x35
TitleMolecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
ComponentsPEREGRIN
KeywordsTRANSCRIPTION / METAL-BINDING / ZINC-FINGER / DNA-BINDING / CHROMATIN REGULATOR / TRANSCRIPTION REGULATION / NUCLEOSOME
Function / homology
Function and homology information


acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / SH3 type barrels. - #140 / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / SH3 type barrels. - #140 / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVezzoli, A. / Bonadies, N. / Allen, M.D. / Freund, S.M.V. / Santiveri, C.M. / Kvinlaug, B. / Huntly, B.J.P. / Gottgens, B. / Bycroft, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Molecular Basis of Histone H3K36Me3 Recognition by the Pwwp Domain of Brpf1.
Authors: Vezzoli, A. / Bonadies, N. / Allen, M.D. / Freund, S.M.V. / Santiveri, C.M. / Kvinlaug, B. / Huntly, B.J.P. / Gottgens, B. / Bycroft, M.
History
DepositionJan 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEREGRIN


Theoretical massNumber of molelcules
Total (without water)15,2501
Polymers15,2501
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.214, 62.399, 114.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PEREGRIN / BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1 / PROTEIN BR140


Mass: 15249.579 Da / Num. of mol.: 1 / Fragment: BRPF1 PWWP DOMAIN, RESIDUES 1076-1205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P55201
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE EXTRA 2 GLYCINES ARE LEFT ON THE PROTEIN AFTER TEV PROTEASE CLEAVAGE

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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: 2.61 Å3/Da / Density % sol: 52.42 % / Description: NONE
Crystal growpH: 8.5
Details: 20% PEG 3350, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 10 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→38.3 Å / Num. obs: 10661 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 26.81 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.2 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.421 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 29.54 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.2359 997 5.1 %
Rwork0.1976 --
obs0.1996 10632 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.098 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 38.99 Å2
Baniso -1Baniso -2Baniso -3
1--11.4582 Å20 Å20 Å2
2--28.4445 Å20 Å2
3----16.9863 Å2
Refinement stepCycle: LAST / Resolution: 2→34.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 64 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131051
X-RAY DIFFRACTIONf_angle_d1.2841423
X-RAY DIFFRACTIONf_dihedral_angle_d15.334406
X-RAY DIFFRACTIONf_chiral_restr0.086151
X-RAY DIFFRACTIONf_plane_restr0.006183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10540.39941190.27952481X-RAY DIFFRACTION88
2.1054-2.23730.25991280.23472599X-RAY DIFFRACTION92
2.2373-2.410.24711610.21122621X-RAY DIFFRACTION94
2.41-2.65250.26311630.20282683X-RAY DIFFRACTION96
2.6525-3.03610.24281480.20832764X-RAY DIFFRACTION98
3.0361-3.82440.19851520.17852780X-RAY DIFFRACTION98
3.8244-34.42570.21261260.17462705X-RAY DIFFRACTION96

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