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- PDB-2x4w: Molecular basis of Histone H3K36me3 recognition by the PWWP domai... -

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Basic information

Entry
Database: PDB / ID: 2x4w
TitleMolecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
Components
  • HISTONE H3.2
  • PEREGRIN
KeywordsTRANSCRIPTION / METAL-BINDING / ZINC-FINGER / CHROMATIN REGULATOR / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding / 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 ...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 / 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 / SH3 type barrels. / Histone-fold / 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
FORMIC ACID / Peregrin / Histone H3.2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionFeb 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: PEREGRIN
B: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6263
Polymers17,5802
Non-polymers461
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10.4 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.261, 71.053, 113.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

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Components

#1: Protein PEREGRIN / BRPF1 PWWP DOMAIN / BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1 / PROTEIN BR140


Mass: 15249.579 Da / Num. of mol.: 1 / Fragment: 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: Protein/peptide HISTONE H3.2 / HUMAN H3 HISTONE / H3/M / H3/O


Mass: 2330.777 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-43 / Source method: obtained synthetically / Details: TRIMETHYLATION AT POSITION 36 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q71DI3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLYSINE 36 IS TRIMETHYLATED

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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: 2.49 Å3/Da / Density % sol: 50.62 % / Description: NONE
Crystal growpH: 8.5 / Details: 4M SODIUM FORMATE, 0.1M TRIS (PH 8.5), 0.01M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.5→35.53 Å / Num. obs: 28447 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 17.37 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.505 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 21.4 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2157 -5 %
Rwork0.1894 --
obs0.1907 28447 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.342 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso mean: 33.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.6774 Å20 Å20 Å2
2--1.8213 Å20 Å2
3----3.4986 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 3 190 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111178
X-RAY DIFFRACTIONf_angle_d1.3551594
X-RAY DIFFRACTIONf_dihedral_angle_d15.68466
X-RAY DIFFRACTIONf_chiral_restr0.093170
X-RAY DIFFRACTIONf_plane_restr0.006203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.52730.25671310.27162664X-RAY DIFFRACTION98
1.5273-1.55670.29051320.25972685X-RAY DIFFRACTION98
1.5567-1.58850.27431730.24032645X-RAY DIFFRACTION99
1.5885-1.6230.23451420.23262680X-RAY DIFFRACTION99
1.623-1.66080.25081200.22142743X-RAY DIFFRACTION99
1.6608-1.70230.24051410.21912673X-RAY DIFFRACTION100
1.7023-1.74830.24821450.20912685X-RAY DIFFRACTION99
1.7483-1.79980.21171580.21312720X-RAY DIFFRACTION100
1.7998-1.85790.2841490.19812700X-RAY DIFFRACTION100
1.8579-1.92430.24461230.19732712X-RAY DIFFRACTION100
1.9243-2.00130.24381150.1952727X-RAY DIFFRACTION100
2.0013-2.09240.23761420.18722715X-RAY DIFFRACTION100
2.0924-2.20270.17861510.17762726X-RAY DIFFRACTION100
2.2027-2.34060.2181520.18482689X-RAY DIFFRACTION100
2.3406-2.52130.25271290.19762760X-RAY DIFFRACTION100
2.5213-2.77490.20951370.19222674X-RAY DIFFRACTION100
2.7749-3.17620.20511340.18352746X-RAY DIFFRACTION100
3.1762-4.00060.15991580.15622683X-RAY DIFFRACTION100
4.0006-33.51310.20041510.17352688X-RAY DIFFRACTION98

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