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- PDB-8sdx: ATAD2B bromodomain in complex with histone H4 acetylated at lysin... -

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Basic information

Entry
Database: PDB / ID: 8sdx
TitleATAD2B bromodomain in complex with histone H4 acetylated at lysine 5 with Serine 1 mutation to Cysteine
Components
  • ATPase family AAA domain-containing protein 2B
  • histone H4S1CK5ac
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: 2.69 Å
AuthorsPhillips, M. / Montgomery, C. / 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 NIH NIGMS United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01CA240685 NIH NCI 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
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: ATPase family AAA domain-containing protein 2B
C: histone H4S1CK5ac
D: histone H4S1CK5ac
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4435
Polymers34,3474
Non-polymers961
Water46826
1
A: ATPase family AAA domain-containing protein 2B
C: histone H4S1CK5ac


Theoretical massNumber of molelcules
Total (without water)17,1742
Polymers17,1742
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-16 kcal/mol
Surface area8630 Å2
MethodPISA
2
B: ATPase family AAA domain-containing protein 2B
D: histone H4S1CK5ac
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2703
Polymers17,1742
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.687, 79.629, 64.348
Angle α, β, γ (deg.)90.000, 105.141, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 15826.093 Da / Num. of mol.: 2 / 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 H4S1CK5ac


Mass: 1347.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 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: 1.072 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.69→33.52 Å / Num. obs: 12940 / % possible obs: 96.47 % / Redundancy: 3.7 % / Biso Wilson estimate: 64.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1244 / Net I/σ(I): 7.63
Reflection shellResolution: 2.69→2.78 Å / Rmerge(I) obs: 1.626 / Num. unique obs: 1036 / CC1/2: 0.374

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→33.52 Å / SU ML: 0.4658 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2604 649 5.17 %
Rwork0.2242 11906 -
obs0.2262 12555 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 5 26 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122347
X-RAY DIFFRACTIONf_angle_d1.40923155
X-RAY DIFFRACTIONf_chiral_restr0.0734358
X-RAY DIFFRACTIONf_plane_restr0.0092410
X-RAY DIFFRACTIONf_dihedral_angle_d24.625930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.90.40481070.36372120X-RAY DIFFRACTION86.15
2.9-3.190.3551460.29562438X-RAY DIFFRACTION99.27
3.19-3.650.3631200.26862442X-RAY DIFFRACTION99.38
3.65-4.60.24121310.20512450X-RAY DIFFRACTION99.04
4.6-33.520.19831450.17572456X-RAY DIFFRACTION98.71

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