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- PDB-9f77: BAZ2A bromodomain in complex with acetylpyrrole derivative compou... -

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Basic information

Entry
Database: PDB / ID: 9f77
TitleBAZ2A bromodomain in complex with acetylpyrrole derivative compound 27-TND19
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / Four helical bundle
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: To Be Published
Title: Unusual backfolded binding poses of BAZ2A bromodomain binders
Authors: Dalle Vedove, A. / Cazzanelli, G. / D'Agostino, V.G. / Caflisch, A. / Lolli, G.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
B: Bromodomain adjacent to zinc finger domain protein 2A
C: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5546
Polymers37,4763
Non-polymers1,0783
Water7,062392
1
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8512
Polymers12,4921
Non-polymers3591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8512
Polymers12,4921
Non-polymers3591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8512
Polymers12,4921
Non-polymers3591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.683, 55.023, 141.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / TTF-I-interacting protein 5 / Tip5 / hWALp3


Mass: 12492.001 Da / Num. of mol.: 3 / Fragment: Bromodomain (residues 1796-1899) / Mutation: E1845H/L1848S
Source method: isolated from a genetically manipulated source
Details: Bromodomain (residues 1796-1899). First two residues SM derive from the expression tag. E1845H/L1848S
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UIF9
#2: Chemical ChemComp-A1H99 / 4-ethanoyl-~{N}-[(1~{S},2~{R})-2-[4-(hydroxymethyl)-1,2,3-triazol-1-yl]cyclohexyl]-3,5-dimethyl-1~{H}-pyrrole-2-carboxamide


Mass: 359.423 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 1.42→70.58 Å / Num. obs: 63350 / % possible obs: 99.5 % / Redundancy: 12.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.028 / Rrim(I) all: 0.099 / Χ2: 0.96 / Net I/σ(I): 14.2 / Num. measured all: 787267
Reflection shellResolution: 1.42→1.44 Å / % possible obs: 99.6 % / Redundancy: 12.4 % / Rmerge(I) obs: 1.593 / Num. measured all: 37744 / Num. unique obs: 3052 / CC1/2: 0.692 / Rpim(I) all: 0.465 / Rrim(I) all: 1.661 / Χ2: 0.9 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→36.523 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 3196 5.05 %
Rwork0.1797 --
obs0.1807 63271 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→36.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 78 392 3023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052849
X-RAY DIFFRACTIONf_angle_d0.8823869
X-RAY DIFFRACTIONf_dihedral_angle_d13.321871
X-RAY DIFFRACTIONf_chiral_restr0.063380
X-RAY DIFFRACTIONf_plane_restr0.004511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.44120.31181300.28412530X-RAY DIFFRACTION99
1.4412-1.46370.25931450.25952527X-RAY DIFFRACTION98
1.4637-1.48770.25311220.22922602X-RAY DIFFRACTION99
1.4877-1.51340.23361440.22292574X-RAY DIFFRACTION99
1.5134-1.54090.21191310.20412525X-RAY DIFFRACTION98
1.5409-1.57050.19141420.19772590X-RAY DIFFRACTION99
1.5705-1.60260.21821340.20042521X-RAY DIFFRACTION99
1.6026-1.63740.20641310.20662615X-RAY DIFFRACTION99
1.6374-1.67550.23321690.19842538X-RAY DIFFRACTION99
1.6755-1.71740.24021430.1982591X-RAY DIFFRACTION99
1.7174-1.76390.21671620.20752566X-RAY DIFFRACTION100
1.7639-1.81580.24891510.19832576X-RAY DIFFRACTION99
1.8158-1.87440.21741330.19392609X-RAY DIFFRACTION99
1.8744-1.94140.18891360.19182626X-RAY DIFFRACTION99
1.9414-2.01910.22911270.1922614X-RAY DIFFRACTION100
2.0191-2.1110.20531400.18572645X-RAY DIFFRACTION100
2.111-2.22220.21861350.17932598X-RAY DIFFRACTION100
2.2222-2.36140.21181140.17652683X-RAY DIFFRACTION100
2.3614-2.54370.21561660.18492608X-RAY DIFFRACTION100
2.5437-2.79960.1991060.18472690X-RAY DIFFRACTION100
2.7996-3.20450.21611290.18032695X-RAY DIFFRACTION100
3.2045-4.03660.17921390.15142714X-RAY DIFFRACTION100
4.0366-36.5230.16141670.16272838X-RAY DIFFRACTION100
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)
10.24250.0976-0.03020.0163-0.0340.07690.02160.02150.00510.0107-0.0198-0.0705-0.02460.15140.00010.17460.02270.03260.17090.00360.185811.206-9.3875-23.3167
20.6109-0.32610.28720.5580.2110.61740.07430.06960.0243-0.0788-0.00560.0961-0.1032-0.17800.15330.00920.0170.1435-0.00190.1536-1.4277-5.5877-19.0665
30.0015-0.0038-0.00640.0090.01420.0223-0.0317-0.11270.25230.30910.125-0.13040.1099-0.01730.00050.23670.0116-0.02360.2748-0.05990.19372.9406-3.5697-0.5853
40.276-0.03570.17510.18180.05980.14610.0283-0.06980.08180.0179-0.0105-0.1948-0.05250.30360.00020.118-0.02010.01880.1547-0.01660.165713.6831-3.0235-15.4735
50.1823-0.06720.09640.2704-0.11510.1130.0686-0.1747-0.08890.00460.0143-0.2914-0.02360.16970.00190.1765-0.0129-0.03460.2226-0.00560.194622.215718.3456-25.5264
60.0060.00560.0040.09380.02880.0011-0.20230.21950.4134-0.034-0.0281-0.0433-0.1992-0.03880.00180.2072-0.0014-0.00890.2230.01410.219511.071427.9857-39.3879
70.3638-0.0641-0.14250.2728-0.12960.14410.104-0.16410.08640.0334-0.09980.0131-0.0136-0.07870.00020.1834-0.02720.01160.1923-0.04460.165413.75824.1416-25.7795
80.2683-0.0221-0.0310.44050.02240.07830.0894-0.0465-0.21280.0393-0.0618-0.00470.3107-0.1559-00.236-0.0219-0.02090.1596-0.00270.18414.435711.9116-29.6635
90.1043-0.0965-0.17370.50190.06450.361-0.00530.2185-0.1043-0.2843-0.06490.0773-0.1549-0.05780.00660.21470.032-0.05960.2199-0.0650.221-1.093426.8688-10.3578
100.37220.1718-0.23860.57880.19960.2759-0.0672-0.0035-0.1583-0.0346-0.0414-0.09560.0661-0.026-00.17660.00480.00120.1621-0.0390.17284.453220.4151-7.3849
110.58830.2475-0.39770.7444-0.59730.5710.111-0.250.20650.2303-0.43050.5395-0.0761-0.4101-0.82510.0758-0.0060.02880.261-0.13770.2535-7.011925.0707-1.0837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1794 through 1818 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1819 through 1872 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1873 through 1877 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1878 through 1899 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1798 through 1818 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1819 through 1839 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1840 through 1872 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1873 through 1898 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1797 through 1829 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1830 through 1872 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1873 through 1898 )

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