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- PDB-6veo: ATAD2B bromodomain in complex with 4-({[(3R,4R)-4-{[3-methyl-5-(5... -

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Basic information

Entry
Database: PDB / ID: 6veo
TitleATAD2B bromodomain in complex with 4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione (compound 38)
ComponentsATPase family AAA domain-containing protein 2B
KeywordsNUCLEAR PROTEIN / Bromodomain / epigenetics
Function / homology
Function and homology information


lysine-acetylated histone binding / histone binding / chromatin binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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 / 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
Chem-YD4 / ATPase family AAA domain-containing protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGlass, 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: 2020
Title: Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain.
Authors: Lloyd, J.T. / McLaughlin, K. / Lubula, M.Y. / Gay, J.C. / Dest, A. / Gao, C. / Phillips, M. / Tonelli, M. / Cornilescu, G. / Marunde, M.R. / Evans, C.M. / Boyson, S.P. / Carlson, S. / Keogh, ...Authors: Lloyd, J.T. / McLaughlin, K. / Lubula, M.Y. / Gay, J.C. / Dest, A. / Gao, C. / Phillips, M. / Tonelli, M. / Cornilescu, G. / Marunde, M.R. / Evans, C.M. / Boyson, S.P. / Carlson, S. / Keogh, M.C. / Markley, J.L. / Frietze, S. / Glass, K.C.
History
DepositionJan 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5304
Polymers15,8261
Non-polymers7043
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-22 kcal/mol
Surface area8230 Å2
Unit cell
Length a, b, c (Å)76.358, 76.358, 102.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-1226-

HOH

21A-1281-

HOH

31A-1299-

HOH

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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 (E. coli) / References: UniProt: Q9ULI0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-YD4 / 4-({[(3R,4R)-4-{[3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl]amino}piperidin-3-yl]oxy}methyl)-1lambda~6~-thiane-1,1-dione


Mass: 511.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H33N5O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG3350, 0.25 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20.24 Å / Num. obs: 13029 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 35.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01997 / Net I/σ(I): 21.51
Reflection shellResolution: 2.4→2.4272 Å / Rmerge(I) obs: 0.6543 / Num. unique obs: 597 / CC1/2: 0.021

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1-3660refinement
PROTEUMdata reduction
PROTEUMdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LXJ

3lxj


Resolution: 2.4→20.24 Å / SU ML: 0.2439 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.6352
RfactorNum. reflection% reflection
Rfree0.2514 640 4.91 %
Rwork0.1939 --
obs0.1965 13029 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 46 100 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531207
X-RAY DIFFRACTIONf_angle_d0.54621638
X-RAY DIFFRACTIONf_chiral_restr0.0504183
X-RAY DIFFRACTIONf_plane_restr0.0043207
X-RAY DIFFRACTIONf_dihedral_angle_d23.9649485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.27461220.26252472X-RAY DIFFRACTION100
2.59-2.840.2651450.25062472X-RAY DIFFRACTION100
2.84-3.250.34021210.22342481X-RAY DIFFRACTION99.85
3.25-4.090.23531300.17612475X-RAY DIFFRACTION99.96
4.1-20.240.21421220.15942489X-RAY DIFFRACTION99.66

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