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- PDB-9ybu: ARID1B ARID bound to compound A-3 (5-(phenylethynyl)pyridine-3-ca... -

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Basic information

Entry
Database: PDB / ID: 9ybu
TitleARID1B ARID bound to compound A-3 (5-(phenylethynyl)pyridine-3-carboxylic acid)
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
5-(phenylethynyl)pyridine-3-carboxylic acid / AT-rich interactive domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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. / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,9683
Polymers13,5211
Non-polymers4462
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.671, 68.671, 46.085
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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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-KVD / 5-(phenylethynyl)pyridine-3-carboxylic acid


Mass: 223.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5 M sodium citrate, pH 6.5, 0.033% w/v 4-nitrobenzoic acid, 0.033% w/v 5-sulfosalicylic acid dihydrate, 0.033% w/v naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 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: CLSI / Beamline: 08ID-1 / Wavelength: 0.953698 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953698 Å / Relative weight: 1
ReflectionResolution: 1.61→36.43 Å / Num. obs: 16160 / % possible obs: 100 % / Redundancy: 20.13 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.052 / Net I/σ(I): 10.9
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 20.29 % / Rmerge(I) obs: 3.076 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1611 / CC1/2: 0.734 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→36.43 Å / SU ML: 0.1664 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 1625 10.07 %
Rwork0.1768 14520 -
obs0.18 16145 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.34 Å2
Refinement stepCycle: LAST / Resolution: 1.61→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 34 93 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061947
X-RAY DIFFRACTIONf_angle_d0.84921273
X-RAY DIFFRACTIONf_chiral_restr0.0472131
X-RAY DIFFRACTIONf_plane_restr0.0065163
X-RAY DIFFRACTIONf_dihedral_angle_d13.2656355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.660.26811370.23381216X-RAY DIFFRACTION100
1.66-1.710.24231300.22391194X-RAY DIFFRACTION99.92
1.71-1.770.25741390.20821209X-RAY DIFFRACTION100
1.77-1.840.22671300.20271194X-RAY DIFFRACTION100
1.84-1.930.25611350.20721202X-RAY DIFFRACTION100
1.93-2.030.2071360.16451198X-RAY DIFFRACTION99.93
2.03-2.160.20221370.17331212X-RAY DIFFRACTION99.93
2.16-2.320.20771340.16161202X-RAY DIFFRACTION100
2.32-2.550.22471350.1851218X-RAY DIFFRACTION100
2.56-2.920.18641340.18151218X-RAY DIFFRACTION100
2.93-3.680.18961390.17181213X-RAY DIFFRACTION99.93
3.69-36.430.19411390.15661244X-RAY DIFFRACTION99.28
Refinement TLS params.Method: refined / Origin x: -22.1879600058 Å / Origin y: 18.4255821041 Å / Origin z: -1.7706373312 Å
111213212223313233
T0.106763978572 Å2-0.00742147579226 Å20.00305996005828 Å2-0.123398010225 Å2-0.00771067973522 Å2--0.104771396421 Å2
L1.49062114575 °2-0.392844409402 °20.6254505027 °2-1.967116147 °2-0.552815533928 °2--1.7306209063 °2
S0.0474423985185 Å °0.0546155288899 Å °-0.0722110400211 Å °-0.0796456595346 Å °0.00654365933095 Å °0.0465501225499 Å °0.0107061201466 Å °0.0358140167158 Å °-0.038135208537 Å °
Refinement TLS groupSelection details: all

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