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

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Basic information

Entry
Database: PDB / ID: 5ffw
TitleCrystal structure of the bromodomain of human BRPF1 in complex with H4K5acK8ac histone peptide
Components
  • Histone H4
  • 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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / 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 / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / 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 / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / 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 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Peregrin / Histone H4 / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 H4K5acK8ac 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 23, 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 H4


Theoretical massNumber of molelcules
Total (without water)28,4093
Polymers28,4093
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-14 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.348, 93.177, 32.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

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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 H4


Mass: 1001.121 Da / Num. of mol.: 1 / Fragment: UNP residues 2-11 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q0VAS5, UniProt: P62805*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.39 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaCl, 25% PEG3350, 0.1 M Hepes pH 7.5 / PH range: 7.5

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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: 1.5→29.26 Å / Num. all: 43114 / Num. obs: 43114 / % possible obs: 99.4 % / Redundancy: 10.8 % / Biso Wilson estimate: 13.698 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.02 / Net I/σ(I): 21.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3.2 / % possible all: 96.2

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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: 1.5→29.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.356 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24307 2137 5 %RANDOM
Rwork0.21223 ---
obs0.21378 40472 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2---1.43 Å20 Å2
3---1.95 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 0 304 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191983
X-RAY DIFFRACTIONr_bond_other_d0.0010.021937
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9872668
X-RAY DIFFRACTIONr_angle_other_deg0.79534451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0225236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61523.832107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74815370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5671519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
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_it1.1921.477932
X-RAY DIFFRACTIONr_mcbond_other1.1921.476931
X-RAY DIFFRACTIONr_mcangle_it1.922.2041163
X-RAY DIFFRACTIONr_mcangle_other1.9192.2051164
X-RAY DIFFRACTIONr_scbond_it1.651.661051
X-RAY DIFFRACTIONr_scbond_other1.6491.6611051
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6782.4231502
X-RAY DIFFRACTIONr_long_range_B_refined5.17913.052620
X-RAY DIFFRACTIONr_long_range_B_other4.96612.1912439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.497→1.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 130 -
Rwork0.267 2790 -
obs--92.03 %
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)
11.2402-1.00460.31141.2406-0.14920.10310.11930.01170.0714-0.0664-0.105-0.18280.0369-0.0213-0.01430.04790.0335-0.01760.06720.00950.0485Chain A65.521936.03827.6877
20.4650.4063-0.16341.21-0.01310.08270.04830.0023-0.00030.0367-0.09260.3041-0.02230.00340.04430.0116-0.00920.00210.0691-0.03150.1148Chain B24.990534.689835.0726
30.29940.45560.08351.89840.66940.3772-0.12690.0889-0.1327-0.28720.1270.05090.05330.0367-0.00010.2194-0.0165-0.05490.0385-0.05080.1609Chain C46.16934.25922.5039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A630 - 739
2X-RAY DIFFRACTION2B629 - 739
3X-RAY DIFFRACTION3C1 - 10

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