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- PDB-3mo8: PWWP Domain of Human Bromodomain and PHD finger-containing protei... -

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Basic information

Entry
Database: PDB / ID: 3mo8
TitlePWWP Domain of Human Bromodomain and PHD finger-containing protein 1 In Complex with Trimethylated H3K36 Peptide
Components
  • Histone H3.2 TRIMETHYLATED H3K36 PEPTIDE
  • Peregrin
KeywordsTRANSCRIPTION / Peregrin / Protein BR140 / histone H3 acetylation / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


spermatogonial cell division / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / regulation of cell differentiation / histone acetyltransferase complex / heterochromatin / Chromatin modifying enzymes ...spermatogonial cell division / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / regulation of cell differentiation / histone acetyltransferase complex / heterochromatin / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / condensed nuclear chromosome / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Peregrin / Histone H3.1t / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsLam, R. / Zeng, H. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Structural and Histone Binding Ability Characterizations of Human PWWP Domains.
Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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 / struct_ref_seq_dif
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

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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 TRIMETHYLATED H3K36 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)16,4332
Polymers16,4332
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.086, 70.605, 113.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsAs per the authors the biological assembly is a monomer

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 15076.455 Da / Num. of mol.: 1 / Fragment: UNP residues 1079-1207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BR140, BRPF1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: P55201
#2: Protein/peptide Histone H3.2 TRIMETHYLATED H3K36 PEPTIDE / Histone H3/m / Histone H3/o


Mass: 1356.615 Da / Num. of mol.: 1 / Fragment: UNP residue 31-42 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3, UniProt: Q16695*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.63 Å3/Da / Density meas: 2.63 Mg/m3 / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3.5M sodium formate, 0.1M Tris-HCl pH8.5, H3K36me3 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 19545 / % possible obs: 99.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.69-1.7460.407196.7
1.74-1.787.20.363199.7
1.78-1.837.70.294199.8
1.83-1.897.90.233199.9
1.89-1.9580.191100
1.95-2.0280.1571100
2.02-2.180.131100
2.1-2.1980.1171100
2.19-2.3180.1011100
2.31-2.4580.0891100
2.45-2.6480.0791100
2.64-2.9180.0681100
2.91-3.337.80.064199.5
3.33-4.197.40.051197.5
4.19-507.20.036197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å40.28 Å
Translation1.98 Å40.28 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L42

3l42


Resolution: 1.69→36.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.05 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20741 1005 5.1 %RANDOM
Rwork0.19167 ---
obs0.19249 18540 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--2.4 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.69→36.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 107 1231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221170
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.9821587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9695141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.12422.552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05715205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.21511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022886
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.771.5703
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44421138
X-RAY DIFFRACTIONr_scbond_it2.1113467
X-RAY DIFFRACTIONr_scangle_it3.5044.5447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 63 -
Rwork0.252 1201 -
obs--87.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82130.187-0.50330.60050.07641.76630.0323-0.0180.0472-0.02290.0287-0.03840.00860.008-0.0610.0624-0.00540.01060.012100.092618.91919.48718.676
21.5390.4753-0.26218.26281.21251.9003-0.06260.08640.127-0.1429-0.00950.2037-0.2913-0.08880.07210.1240.0110.0030.01770.03070.098413.44929.73613.306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1078 - 1204
2X-RAY DIFFRACTION2B1 - 12

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