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- PDB-4qyd: Crystal Structure of the human BRPF1 bromodomain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4qyd
TitleCrystal Structure of the human BRPF1 bromodomain in complex with a histone H4K12ac peptide
Components
  • Histone H4
  • Peregrin
KeywordsPROTEIN BINDING / bromodomain-PHD finger protein 1 (BRPF1) / histone acetyltransferase (HAT) / monocytic leukemia zinc-finger (MOZ) / epigenetics / chromatin reader / bromodomain / histone post-transcriptional modification (PTM) reader domain / histone H4 acetylated at lysine 14 / acetyllysine / nucleus
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 / Regulation of TP53 Activity through Acetylation / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / 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 / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / RNA 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Peregrin / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLubula, M.Y. / Glass, K.C.
CitationJournal: Febs Lett. / Year: 2014
Title: Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain.
Authors: Lubula, M.Y. / Eckenroth, B.E. / Carlson, S. / Poplawski, A. / Chruszcz, M. / Glass, K.C.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Sep 20, 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peregrin
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)15,0372
Polymers15,0372
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.100, 75.100, 86.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-324-

HOH

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Components

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


Mass: 13720.686 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 629-742)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BR140, BRPF1 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Protein/peptide Histone H4


Mass: 1316.555 Da / Num. of mol.: 1 / Fragment: histone H4K12ac peptide (UNP residues 5-18) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 10% w/v polyethylene glycol (PEG) 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.94→34.43 Å / Num. obs: 18780 / % possible obs: 99.9 % / Observed criterion σ(I): 14.66 / Redundancy: 27.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 25.84
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 27.2 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 14.66 / % possible all: 96.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1402)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D9E

2d9e


Resolution: 1.94→34.43 Å / SU ML: 0.12 / σ(F): 1.37 / Phase error: 18.93 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.213 966 5.14 %
Rwork0.175 --
obs0.177 18780 99.7 %
all-18780 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms995 0 0 143 1138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071014
X-RAY DIFFRACTIONf_angle_d0.951361
X-RAY DIFFRACTIONf_dihedral_angle_d12.875392
X-RAY DIFFRACTIONf_chiral_restr0.066146
X-RAY DIFFRACTIONf_plane_restr0.004179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.04350.20921290.17092475X-RAY DIFFRACTION98
2.0435-2.17150.21781240.16312494X-RAY DIFFRACTION100
2.1715-2.33920.18271520.172496X-RAY DIFFRACTION100
2.3392-2.57450.18621420.17242509X-RAY DIFFRACTION100
2.5745-2.94690.23231360.18792554X-RAY DIFFRACTION100
2.9469-3.7120.21741280.17512584X-RAY DIFFRACTION100
3.712-34.43340.22141550.17632702X-RAY DIFFRACTION100
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)
15.4108-1.2440.01556.00420.53564.3278-0.1516-2.1388-0.04821.3247-0.03-1.07120.65231.1199-0.01070.22110.1663-0.1110.82820.1760.277125.479784.2492100.5969
25.8942-1.547-1.82343.86170.28832.0082-0.1071-0.7629-0.25570.22650.04970.3069-0.05140.02810.05260.17930.00990.04980.278-0.00390.17894.012490.751999.5984
33.5762-0.5241-1.25261.97870.54192.5334-0.2054-0.6827-0.75730.23740.1920.21450.3570.2452-0.00420.21280.02980.04170.28580.08930.247614.549284.080196.1942
47.2357-1.752-1.49592.9130.79232.3630.3091-0.31351.07510.06480.0151-0.4337-0.2590.1843-0.28660.1648-0.03450.02350.1795-0.01610.206517.784796.133192.6837
55.03654.41415.26934.48453.99376.1669-0.087-0.769-1.6659-0.39260.9089-0.67381.13380.8484-0.65260.58340.1729-0.09410.83540.00891.001831.240677.454489.4081
66.8979-2.2711-0.09676.5191-4.97174.33630.0720.70450.5537-0.501-0.1674-0.25220.3496-0.6770.10830.20760.05130.04610.3938-0.02270.1733-1.736398.013794.6083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 117 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 13 )

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