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- PDB-8uhl: ATAD2B bromodomain in complex with histone H4 acetylated at lysine 12 -

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Basic information

Entry
Database: PDB / ID: 8uhl
TitleATAD2B bromodomain in complex with histone H4 acetylated at lysine 12
Components
  • ATPase family AAA domain-containing protein 2B
  • Histone H4
KeywordsNUCLEAR PROTEIN / bromodomains / Epigenetics / chromatin reader domain / protein binding
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: 1.92 Å
AuthorsPhillips, M. / Montgomery, C. / Nix, J.C. / Glass, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129338 NIH NIGMS 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 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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 H4
C: Histone H4


Theoretical massNumber of molelcules
Total (without water)18,4593
Polymers18,4593
Non-polymers00
Water1,802100
1
A: ATPase family AAA domain-containing protein 2B
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)17,1432
Polymers17,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-6 kcal/mol
Surface area8560 Å2
MethodPISA
2
C: Histone H4


  • defined by author&software
  • 1.32 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,3171
Polymers1,3171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.119, 55.119, 140.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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 (bacteria) / References: UniProt: Q9ULI0
#2: Protein/peptide Histone H4


Mass: 1316.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic pH 7

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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 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→27.56 Å / Num. obs: 17341 / % possible obs: 99.68 % / Redundancy: 13 % / Biso Wilson estimate: 34.61 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1091 / Rpim(I) all: 0.03137 / Rrim(I) all: 0.1136 / Net I/σ(I): 20.22
Reflection shellResolution: 1.92→1.989 Å / Num. unique obs: 1672 / CC1/2: 0.448 / CC star: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→27.56 Å / Cross valid method: FREE R-VALUE / Phase error: 23.3546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 --
Rwork0.2003 14656 -
obs-17341 99.68 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.69 Å2
Refinement stepCycle: LAST / Resolution: 1.92→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 100 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941250
X-RAY DIFFRACTIONf_angle_d1.03991679
X-RAY DIFFRACTIONf_chiral_restr0.0595189
X-RAY DIFFRACTIONf_plane_restr0.0062219
X-RAY DIFFRACTIONf_dihedral_angle_d19.4036504

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