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- PDB-8sdo: ATAD2 bromodomain in complex with "oncohistone" mutation H4S1CK5a... -

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Basic information

Entry
Database: PDB / ID: 8sdo
TitleATAD2 bromodomain in complex with "oncohistone" mutation H4S1CK5ac (res 1-15) ligand
Components
  • ATPase family AAA domain-containing protein 2
  • Histone H4
KeywordsPROTEIN BINDING / Bromodomain / epigenetics / Nuclear protein / cancer / histone mutations
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / 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 / Bromodomain profile. / bromo domain ...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 / Bromodomain profile. / bromo domain / Bromodomain / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMalone, K.L. / 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
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2
B: Histone H4


Theoretical massNumber of molelcules
Total (without water)19,2062
Polymers19,2062
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-6 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.941, 53.941, 159.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-1350-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 17858.201 Da / Num. of mol.: 1 / Mutation: C1101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q6PL18, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide Histone H4


Mass: 1347.570 Da / Num. of mol.: 1 / Mutation: S1C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2.4 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.01→27.46 Å / Num. obs: 16480 / % possible obs: 99.51 % / Redundancy: 13.4 % / Biso Wilson estimate: 43.36 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 18.91
Reflection shellResolution: 2.01→2.082 Å / Num. unique obs: 1529 / CC1/2: 0.372

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→27.46 Å / SU ML: 0.2562 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 762 4.64 %
Rwork0.2007 15649 -
obs0.2021 16411 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.87 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 0 168 1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641161
X-RAY DIFFRACTIONf_angle_d0.89041568
X-RAY DIFFRACTIONf_chiral_restr0.0503172
X-RAY DIFFRACTIONf_plane_restr0.0071210
X-RAY DIFFRACTIONf_dihedral_angle_d26.9932461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.160.30571640.28242965X-RAY DIFFRACTION97.96
2.17-2.380.30461460.2753069X-RAY DIFFRACTION99.88
2.38-2.730.22751430.20123108X-RAY DIFFRACTION99.97
2.73-3.440.25511640.20643139X-RAY DIFFRACTION100
3.44-27.460.19811450.17973368X-RAY DIFFRACTION100

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