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- PDB-7m98: ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand -

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Basic information

Entry
Database: PDB / ID: 7m98
TitleATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand
Components
  • ATPase family AAA domain-containing protein 2
  • Histone H4
KeywordsNUCLEAR PROTEIN / Bromodomain / epigenetics
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / 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. / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor ...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. / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Histone-fold / 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
Histone H4 / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMalone, K.L. / 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: Int J Mol Sci / Year: 2021
Title: Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain.
Authors: Evans, C.M. / Phillips, M. / Malone, K.L. / Tonelli, M. / Cornilescu, G. / Cornilescu, C. / Holton, S.J. / Gorjanacz, M. / Wang, L. / Carlson, S. / Gay, J.C. / Nix, J.C. / Demeler, B. / ...Authors: Evans, C.M. / Phillips, M. / Malone, K.L. / Tonelli, M. / Cornilescu, G. / Cornilescu, C. / Holton, S.J. / Gorjanacz, M. / Wang, L. / Carlson, S. / Gay, J.C. / Nix, J.C. / Demeler, B. / Markley, J.L. / Glass, K.C.
History
DepositionMar 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)19,1902
Polymers19,1902
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.560, 53.560, 160.350
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

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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-6P1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q6PL18, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide Histone H4


Mass: 1331.505 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P62805
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6

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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 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→44.54 Å / Num. obs: 32508 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 26.92 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.0178 / Rrim(I) all: 0.136 / Net I/σ(I): 18.87
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6612 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 3090 / CC1/2: 0.495 / CC star: 0.814 / Rpim(I) all: 0.6612 / Rrim(I) all: 0.935 / % possible all: 97.14

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TT2

4tt2


Resolution: 1.6→44.54 Å / SU ML: 0.195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2187 1612 5.07 %
Rwork0.194 30172 -
obs0.1953 31784 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 203 1360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01371227
X-RAY DIFFRACTIONf_angle_d1.25031659
X-RAY DIFFRACTIONf_chiral_restr0.0759181
X-RAY DIFFRACTIONf_plane_restr0.0085222
X-RAY DIFFRACTIONf_dihedral_angle_d22.2272503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.34231110.31672429X-RAY DIFFRACTION98.37
1.65-1.70.27911420.2832426X-RAY DIFFRACTION99.88
1.7-1.760.26961220.24382506X-RAY DIFFRACTION99.96
1.76-1.830.26261270.2412457X-RAY DIFFRACTION100
1.83-1.910.32361370.30392483X-RAY DIFFRACTION99.81
1.91-2.020.27511410.24782477X-RAY DIFFRACTION100
2.02-2.140.22721390.18992511X-RAY DIFFRACTION100
2.14-2.310.21811380.20442472X-RAY DIFFRACTION99.77
2.31-2.540.21121250.18922541X-RAY DIFFRACTION100
2.54-2.910.19361450.19182521X-RAY DIFFRACTION100
2.91-3.660.2171290.17782589X-RAY DIFFRACTION100
3.66-44.540.19831560.16822760X-RAY DIFFRACTION99.97

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