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- PDB-4qut: Structure of the bromodomain of human ATPase family AAA domain-co... -

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Basic information

Entry
Database: PDB / ID: 4qut
TitleStructure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12
Components
  • ATPase family AAA domain-containing protein 2
  • Histone H4
KeywordsSIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / bromodomain / actyl-lysine binding / ATPase family AAA domain-containing protein 2 / epigenetics / histone / bromodomain-histone / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


nucleosome disassembly / 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 ...nucleosome disassembly / 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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Meiotic synapsis / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / transcription initiation-coupled chromatin remodeling / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / nucleosome assembly / structural constituent of chromatin / nucleosome / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / histone binding / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane
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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 ...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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / ATPase family associated with various cellular activities (AAA) / Bromodomain-like / ATPase, AAA-type, core / Histone Acetyltransferase; Chain A / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChaikuad, A. / Felletar, I. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J Mol Cell Biol / Year: 2016
Title: Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells.
Authors: Morozumi, Y. / Boussouar, F. / Tan, M. / Chaikuad, A. / Jamshidikia, M. / Colak, G. / He, H. / Nie, L. / Petosa, C. / de Dieuleveult, M. / Curtet, S. / Vitte, A.L. / Rabatel, C. / ...Authors: Morozumi, Y. / Boussouar, F. / Tan, M. / Chaikuad, A. / Jamshidikia, M. / Colak, G. / He, H. / Nie, L. / Petosa, C. / de Dieuleveult, M. / Curtet, S. / Vitte, A.L. / Rabatel, C. / Debernardi, A. / Cosset, F.L. / Verhoeyen, E. / Emadali, A. / Schweifer, N. / Gianni, D. / Gut, M. / Guardiola, P. / Rousseaux, S. / Gerard, M. / Knapp, S. / Zhao, Y. / Khochbin, S.
History
DepositionJul 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,99614
Polymers16,2172
Non-polymers77912
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-1 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.980, 78.980, 139.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1433-

HOH

21A-1458-

HOH

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Components

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


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain (residues 981-1108)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-R3-pRARE2 / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Protein/peptide Histone H4


Mass: 763.841 Da / Num. of mol.: 1 / Fragment: histone H4 tail / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, ...Details: apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 13, 2012
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→34.34 Å / Num. all: 28321 / Num. obs: 28319 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3895 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id: 3DAI

3dai


Resolution: 1.7→34.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.705 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17952 1441 5.1 %RANDOM
Rwork0.16231 ---
all0.189 28319 --
obs0.16319 26877 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å20 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 49 261 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191283
X-RAY DIFFRACTIONr_bond_other_d0.0010.021275
X-RAY DIFFRACTIONr_angle_refined_deg1.5482.0131725
X-RAY DIFFRACTIONr_angle_other_deg0.84932953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8435163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3123.09971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60815247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2581518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_mcbond_it1.1731.188570
X-RAY DIFFRACTIONr_mcbond_other1.0811.179569
X-RAY DIFFRACTIONr_mcangle_it1.7941.764717
X-RAY DIFFRACTIONr_mcangle_other1.8151.77718
X-RAY DIFFRACTIONr_scbond_it2.1071.604713
X-RAY DIFFRACTIONr_scbond_other2.1071.604713
X-RAY DIFFRACTIONr_scangle_other3.1562.187993
X-RAY DIFFRACTIONr_long_range_B_refined9.98613.4641764
X-RAY DIFFRACTIONr_long_range_B_other9.98413.4841765
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 118 -
Rwork0.353 1784 -
obs--91.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
146.3253-9.572928.095816.47971.446130.5533-1.0162-1.56241.61010.409-0.45011.2903-0.5465-2.08971.46620.13550.05930.10360.307-0.03060.5033-9.69245.0886.598
21.2444-0.4345-1.16740.67290.34641.82130.02990.0950.0323-0.05930.00730.0035-0.02850.023-0.03730.01760.0052-0.00610.05860.00770.027316.65442.01-4.966
310.58641.83521.84922.70210.13733.5028-0.08170.6409-0.0588-0.23330.11940.11850.1263-0.1406-0.03770.0432-0.01780.01240.1025-0.00510.0413-2.4234.8941.961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A979 - 984
2X-RAY DIFFRACTION2A985 - 1090
3X-RAY DIFFRACTION2B9 - 13
4X-RAY DIFFRACTION3A1091 - 1108

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