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- PDB-2x4x: Molecular basis of Histone H3K36me3 recognition by the PWWP domai... -

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Basic information

Entry
Database: PDB / ID: 2x4x
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 / NUCLEOSOME
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 / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / 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 / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / 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 ...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 C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / SH3 type barrels. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Bromodomain, conserved site / Bromodomain signature. / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Peregrin / Histone H3.2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.1Jun 9, 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
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: PEREGRIN
D: HISTONE H3.2
E: PEREGRIN
F: HISTONE H3.2
G: PEREGRIN
H: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4179
Polymers70,3218
Non-polymers961
Water10,341574
1
E: PEREGRIN
F: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-12.3 kcal/mol
Surface area8400 Å2
MethodPISA
2
C: PEREGRIN
D: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11.2 kcal/mol
Surface area8330 Å2
MethodPISA
3
G: PEREGRIN
H: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11.1 kcal/mol
Surface area8250 Å2
MethodPISA
4
A: PEREGRIN
B: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6763
Polymers17,5802
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-21.8 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.437, 102.941, 88.654
Angle α, β, γ (deg.)90.00, 100.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15249.579 Da / Num. of mol.: 4 / 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: Protein/peptide
HISTONE H3.2 / HUMAN H3 HISTONE / H3/M / H3/O


Mass: 2330.777 Da / Num. of mol.: 4 / Fragment: RESIDUES 23-43 / Source method: obtained synthetically / Details: TRIMETHYLATION AT POSITION 36 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q71DI3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.45 Å3/Da / Density % sol: 49.87 % / Description: NONE
Crystal growpH: 8.5
Details: 20% PEG3350, 0.2M LITHIUM SULPHATE, 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: 1.85→44.32 Å / Num. obs: 57772 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→34.998 Å / SU ML: 0.25 / σ(F): 1.31 / Phase error: 25.54 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2391 5393 5 %
Rwork0.1969 --
obs0.1991 57745 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.734 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 33.99 Å2
Baniso -1Baniso -2Baniso -3
1-4.3873 Å2-0 Å26.8587 Å2
2---3.8323 Å20 Å2
3----0.555 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 5 574 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014573
X-RAY DIFFRACTIONf_angle_d1.2596197
X-RAY DIFFRACTIONf_dihedral_angle_d16.5751783
X-RAY DIFFRACTIONf_chiral_restr0.094653
X-RAY DIFFRACTIONf_plane_restr0.006792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.28231470.27373326X-RAY DIFFRACTION91
1.871-1.8930.32211680.26193322X-RAY DIFFRACTION92
1.893-1.91610.28481920.25873355X-RAY DIFFRACTION92
1.9161-1.94040.29821890.25093281X-RAY DIFFRACTION92
1.9404-1.96590.30461960.24473298X-RAY DIFFRACTION93
1.9659-1.99280.2961940.24693329X-RAY DIFFRACTION93
1.9928-2.02130.30991610.24463464X-RAY DIFFRACTION93
2.0213-2.05150.25711570.23023330X-RAY DIFFRACTION93
2.0515-2.08350.26831640.2343311X-RAY DIFFRACTION93
2.0835-2.11770.281970.22533464X-RAY DIFFRACTION94
2.1177-2.15420.24771810.20843338X-RAY DIFFRACTION93
2.1542-2.19340.25621700.20193382X-RAY DIFFRACTION94
2.1934-2.23550.3061600.1973476X-RAY DIFFRACTION94
2.2355-2.28120.23821890.19253399X-RAY DIFFRACTION94
2.2812-2.33070.25671720.18363363X-RAY DIFFRACTION94
2.3307-2.3850.23191730.19943483X-RAY DIFFRACTION94
2.385-2.44460.28131590.2113381X-RAY DIFFRACTION95
2.4446-2.51070.27261800.21013412X-RAY DIFFRACTION95
2.5107-2.58450.2612090.21663443X-RAY DIFFRACTION95
2.5845-2.66790.28291760.21173396X-RAY DIFFRACTION96
2.6679-2.76320.28441700.19883515X-RAY DIFFRACTION95
2.7632-2.87380.24031920.19513397X-RAY DIFFRACTION95
2.8738-3.00450.24411730.20433475X-RAY DIFFRACTION96
3.0045-3.16280.2511850.20573527X-RAY DIFFRACTION97
3.1628-3.36090.21751810.18673483X-RAY DIFFRACTION97
3.3609-3.62010.23161790.17353495X-RAY DIFFRACTION97
3.6201-3.9840.22241840.17033528X-RAY DIFFRACTION97
3.984-4.55940.18842330.1593472X-RAY DIFFRACTION97
4.5594-5.74020.18561750.17143545X-RAY DIFFRACTION98
5.7402-35.00390.19241870.18733411X-RAY DIFFRACTION95

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