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- PDB-5ffv: Crystal structure of the bromodomain of human BRPF1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5ffv
TitleCrystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide
Components
  • Histone H3
  • Peregrin
KeywordsTRANSCRIPTION / Peregrin / MOZ-MORF complex
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 / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening ...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 / telomere organization / 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 / epigenetic regulation of gene 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 / gene expression / Estrogen-dependent gene expression / cadherin binding / 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 / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / 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 / : / : / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H3 / Peregrin / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTallant, C. / Nunez-Alonso, G. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide
Authors: Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
History
DepositionDec 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peregrin
B: Peregrin
C: Histone H3
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9987
Polymers29,8124
Non-polymers1863
Water4,936274
1
A: Peregrin
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0304
Polymers14,9062
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area7410 Å2
MethodPISA
2
B: Peregrin
D: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9683
Polymers14,9062
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.266, 74.354, 49.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 13703.698 Da / Num. of mol.: 2 / Fragment: UNP residues 626-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Protein/peptide Histone H3


Mass: 1202.384 Da / Num. of mol.: 2 / Fragment: UNP residues 10-20 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3, UniProt: P68431*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.77 % / Description: Rod
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 0.2 M MgCl2, 0.1 M bis-tris pH 5.5 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→29.73 Å / Num. all: 67343 / Num. obs: 67343 / % possible obs: 98.6 % / Redundancy: 11.1 % / Biso Wilson estimate: 13.37 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.027 / Net I/σ(I): 17.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.5 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.3→29.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.364 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20636 3307 4.9 %RANDOM
Rwork0.18997 ---
obs0.19077 63980 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å20 Å2
2---0.34 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.3→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 12 274 2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192005
X-RAY DIFFRACTIONr_bond_other_d0.0010.021946
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9872693
X-RAY DIFFRACTIONr_angle_other_deg0.77634470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0765235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33623.832107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48315360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2591519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
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_it1.0461.435946
X-RAY DIFFRACTIONr_mcbond_other1.0431.433945
X-RAY DIFFRACTIONr_mcangle_it1.6422.1371179
X-RAY DIFFRACTIONr_mcangle_other1.6422.1391180
X-RAY DIFFRACTIONr_scbond_it1.7311.6241059
X-RAY DIFFRACTIONr_scbond_other1.7311.6241059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7162.3661515
X-RAY DIFFRACTIONr_long_range_B_refined4.79912.5182619
X-RAY DIFFRACTIONr_long_range_B_other4.59711.8322443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 247 -
Rwork0.226 3938 -
obs--83.62 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.7360.255-0.02610.6890.01760.1151-0.01280.0309-0.0254-0.0263-0.0219-0.04210.0380.0250.03470.01630.00520.01450.02030.00740.0139Chain A62.410510.569631.3339
20.6174-0.1631-0.12690.60940.09090.1389-0.0299-0.01490.08940.04520.0296-0.0261-0.0058-0.0550.00030.00630.0113-0.00720.036-0.01310.0164Chain B46.683423.951843.1319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A630 - 737
2X-RAY DIFFRACTION2B630 - 737

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