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- PDB-9ybw: ARID1B ARID bound to compound B-2 ((2M)-2'-(morpholin-4-yl)-6-oxo... -

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Basic information

Entry
Database: PDB / ID: 9ybw
TitleARID1B ARID bound to compound B-2 ((2M)-2'-(morpholin-4-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydro[2,3'-bipyridine]-5-carbonitrile)
ComponentsAT-rich interactive domain-containing protein 1B
KeywordsDNA BINDING PROTEIN / ARID / BAF
Function / homology
Function and homology information


brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / regulation of G0 to G1 transition / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / regulation of nucleotide-excision repair / positive regulation of double-strand break repair ...brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / regulation of G0 to G1 transition / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / regulation of nucleotide-excision repair / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of myoblast differentiation / regulation of G1/S transition of mitotic cell cycle / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RMTs methylate histone arginines / nervous system development / transcription coactivator activity / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / DNA binding / nucleoplasm
Similarity search - Function
AT-rich interactive domain-containing protein 1B / SWI/SNF-like complex subunit BAF250/Osa / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain
Similarity search - Domain/homology
: / ACETATE ION / AT-rich interactive domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCarbone, C.E. / Holliday, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryptic Small Molecule Binding Sites in the ARID1B DNA Binding Domain
Authors: Holliday, M.J. / Carbone, C.E. / Pierce, L. / Zhao, V.Y. / Schoenherr, H.
History
DepositionSep 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AT-rich interactive domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,44111
Polymers13,5211
Non-polymers92010
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.320, 90.320, 37.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-1202-

ZN

21A-1340-

HOH

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Components

#1: Protein AT-rich interactive domain-containing protein 1B / ARID domain-containing protein 1B / BRG1-associated factor 250b / BAF250B / BRG1-binding protein ...ARID domain-containing protein 1B / BRG1-associated factor 250b / BAF250B / BRG1-binding protein hELD/OSA1 / Osa homolog 2 / hOsa2 / p250R


Mass: 13521.431 Da / Num. of mol.: 1 / Fragment: UNP residues 1124-1242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1B, BAF250B, DAN15, KIAA1235, OSA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NFD5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-A1CUA / (2M)-2'-(morpholin-4-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydro[2,3'-bipyridine]-5-carbonitrile


Mass: 350.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13F3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10.7% PEG3350, 0.044 M zinc acetate, 0.025% w/v 3,5-dinitrosalicylic acid, 0.025% w/v 4-aminobenzoic acid, 0.025% w/v salicylic acid, 0.025% w/v trimesic acid, 0.002 M HEPES sodium, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 1.88→64.04 Å / Num. obs: 13242 / % possible obs: 99.65 % / Redundancy: 16.28 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.031 / Net I/σ(I): 13.5
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 15.61 % / Rmerge(I) obs: 2.067 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1273 / CC1/2: 0.592 / % possible all: 99.22

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→63.87 Å / SU ML: 0.2853 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 1321 10 %
Rwork0.2004 11889 -
obs0.2047 13210 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.15 Å2
Refinement stepCycle: LAST / Resolution: 1.88→63.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 43 56 902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112857
X-RAY DIFFRACTIONf_angle_d1.2281155
X-RAY DIFFRACTIONf_chiral_restr0.0503118
X-RAY DIFFRACTIONf_plane_restr0.0148147
X-RAY DIFFRACTIONf_dihedral_angle_d19.508327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.960.3211410.31272X-RAY DIFFRACTION100
1.96-2.040.32371430.27361285X-RAY DIFFRACTION100
2.04-2.150.29431440.28911298X-RAY DIFFRACTION99.93
2.15-2.290.341440.29681297X-RAY DIFFRACTION100
2.29-2.460.31231450.24461313X-RAY DIFFRACTION99.79
2.46-2.710.20341480.16871318X-RAY DIFFRACTION99.93
2.71-3.10.22481450.19341318X-RAY DIFFRACTION100
3.1-3.910.23761500.18641350X-RAY DIFFRACTION100
3.91-63.870.21951610.16811438X-RAY DIFFRACTION99.94
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)
17.96619264649-3.435835393190.02531549806443.26874704757-1.177238334316.77245368532-0.177071007159-1.07016752961-0.9360280368380.9327236472850.2155069331130.1321318126370.7743807496340.113162563689-0.01870434484130.3698010914880.0132327839189-0.05189139950190.2678679202950.05653310638120.4249111096125.8833987305425.05200548159.1237046779
21.10487326396-0.065332633651-0.6178802075210.8308586370730.02228222768370.3291195080540.321913443330.9945240867310.30689258173-0.482153027897-0.20208135164-0.0732502485525-0.10047335863-0.584935791568-0.09475989447830.4099675714270.0463354189722-0.04756330070350.476501843871-0.04199623175310.5028021051443.6002808253928.0262581284-3.7096756938
39.19044385404-1.52520909312-1.8858735524.16876350721-0.7266973214092.77833723809-0.0473072957172-0.00856075086901-0.156256212556-0.1260849353610.254379977551-0.226069288977-0.04537916653440.0673885835822-0.01546920257420.2362413814510.0507518773923-0.001745754446520.266157492782-0.005972850352040.19633736781816.91395245325.07165342891.93238860287
44.5141509224-0.966224378261-0.4382205009955.827785654821.894946244215.802382716610.1588492819860.1666787884810.0211691300172-0.224820757878-0.0676221257661-0.2435919030060.07592298586210.226578902704-0.02181384296860.2028202879570.0480708438766-0.02673269752530.1703587981290.06101396030690.21920671630716.245059215731.4063946937-1.63990855003
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1053 through 1069 )1053 - 10691 - 17
22chain 'A' and (resid 1070 through 1086 )1070 - 108618 - 34
33chain 'A' and (resid 1087 through 1097 )1087 - 109735 - 45
44chain 'A' and (resid 1098 through 1152 )1098 - 115246 - 100

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