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- PDB-8uk5: Crystal structure of the bromodomain of human ATAD2B in complex w... -

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Basic information

Entry
Database: PDB / ID: 8uk5
TitleCrystal structure of the bromodomain of human ATAD2B in complex with histone H4S1(ph)K5ac
Components
  • ATPase family AAA domain-containing protein 2B
  • Histone H4S1(ph)K5ac
KeywordsPEPTIDE BINDING PROTEIN / bromodomain / epigenetics / chromatin reader domain / PROTEIN BINDING / histone acetylation
Function / homology
Function and homology information


nucleosome disassembly / : / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATPase family AAA domain-containing protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMontgomery, C. / Phillips, M. / Nix, J.C. / Glass, K.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129338 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM104865 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains.
Authors: Phillips, M. / Malone, K.L. / Boyle, B.W. / Montgomery, C. / Kressy, I.A. / Joseph, F.M. / Bright, K.M. / Boyson, S.P. / Chang, S. / Nix, J.C. / Young, N.L. / Jeffers, V. / Frietze, S. / Glass, K.C.
History
DepositionOct 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2B
B: Histone H4S1(ph)K5ac


Theoretical massNumber of molelcules
Total (without water)17,1662
Polymers17,1662
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.080, 48.580, 83.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ATPase family AAA domain-containing protein 2B


Mass: 15826.093 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 953-1085)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2B, KIAA1240
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9ULI0
#2: Protein/peptide Histone H4S1(ph)K5ac


Mass: 1340.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS (pH 5.5), 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→31.37 Å / Num. obs: 33447 / % possible obs: 99.51 % / Redundancy: 11.9 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 28.93
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 37316 / CC1/2: 0.873 / CC star: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→31.37 Å / SU ML: 0.1418 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2023 --
Rwork0.1784 31755 -
obs-33447 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.77 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 0 268 1370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841150
X-RAY DIFFRACTIONf_angle_d0.86451557
X-RAY DIFFRACTIONf_chiral_restr0.0663179
X-RAY DIFFRACTIONf_plane_restr0.0066203
X-RAY DIFFRACTIONf_dihedral_angle_d12.887447
LS refinement shellResolution: 3.2→31.37 Å
RfactorNum. reflection% reflection
Rfree0.1689 135 -
Rwork0.1626 2814 -
obs--98.89 %

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