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

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Basic information

Entry
Database: PDB / ID: 4qyl
TitleCrystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide
Components
  • Histone H2A type 1
  • 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 / acetyllysine / nucleus
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / histone H3-K23 acetylation / histone H3-K14 acetylation / histone acetyltransferase complex / heterochromatin assembly => GO:0031507 / HCMV Late Events / histone H3 acetylation / Regulation of TP53 Activity through Acetylation / HDACs deacetylate histones ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / histone H3-K23 acetylation / histone H3-K14 acetylation / histone acetyltransferase complex / heterochromatin assembly => GO:0031507 / HCMV Late Events / histone H3 acetylation / Regulation of TP53 Activity through Acetylation / HDACs deacetylate histones / Metalloprotease DUBs / RMTs methylate histone arginines / HCMV Early Events / nucleosome / UCH proteinases / HATs acetylate histones / histone binding / chromosome / Ub-specific processing proteases / protein heterodimerization activity / positive regulation of transcription, DNA-templated / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / plasma membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / BR140-related, PWWD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / domain with conserved PWWP motif / PWWP domain / PWWP domain / PWWP domain profile. / Extended PHD (ePHD) domain ...BRPF1, PHD domain / Peregrin, ePHD domain / BR140-related, PWWD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / domain with conserved PWWP motif / PWWP domain / PWWP domain / PWWP domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Histone H2A conserved site / Histone H2A signature. / Zinc finger C2H2 type domain profile. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / PHD zinc finger / Zinc finger, PHD-type / Histone-fold / Zinc finger, FYVE/PHD-type / Bromodomain-like / Histone Acetyltransferase; Chain A / 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
Histone H2A type 1 / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peregrin
B: Peregrin
C: Peregrin
D: Peregrin
E: Histone H2A type 1
F: Histone H2A type 1
G: Histone H2A type 1
H: Histone H2A type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,13612
Polymers59,7528
Non-polymers3844
Water13,007722
1
A: Peregrin
E: Histone H2A type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0343
Polymers14,9382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-19 kcal/mol
Surface area7630 Å2
MethodPISA
2
B: Peregrin
F: Histone H2A type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0343
Polymers14,9382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-17 kcal/mol
Surface area7730 Å2
MethodPISA
3
C: Peregrin
G: Histone H2A type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0343
Polymers14,9382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-17 kcal/mol
Surface area7550 Å2
MethodPISA
4
D: Peregrin
H: Histone H2A type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0343
Polymers14,9382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-18 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)60.908, 55.581, 82.135
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 117
2010B1 - 117
1020A1 - 117
2020C1 - 117
1030A1 - 117
2030D1 - 117
1040B1 - 117
2040C1 - 117
1050B1 - 117
2050D1 - 117
1060C1 - 117
2060D1 - 117

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 13720.686 Da / Num. of mol.: 4 / 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) / Strain (production host): Rosetta2DE3pLysS / References: UniProt: P55201
#2: Protein/peptide
Histone H2A type 1 / H2A.1 / Histone H2A/p


Mass: 1217.361 Da / Num. of mol.: 4 / Fragment: histone H2AK5ac peptide (UNP residues 2-13) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0C0S8
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, 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 Å
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: 1.8→41.02 Å / Num. all: 48421 / Num. obs: 48421 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.04
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RCW
Resolution: 1.8→41.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.095 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25257 2587 5.1 %RANDOM
Rwork0.20389 ---
obs0.20629 48421 99.97 %-
all-48421 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0.09 Å2
2--0.66 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 20 722 4829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194354
X-RAY DIFFRACTIONr_bond_other_d0.0080.024147
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9885881
X-RAY DIFFRACTIONr_angle_other_deg1.35139554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.895539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97124.764233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26315778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2871533
X-RAY DIFFRACTIONr_chiral_restr0.1120.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215060
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021033
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A75100.07
12B75100.07
21A73700.08
22C73700.08
31A73840.07
32D73840.07
41B72140.07
42C72140.07
51B72280.07
52D72280.07
61C71590.09
62D71590.09
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 197 -
Rwork0.25 3536 -
obs--100 %

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