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- PDB-9ybs: ARID1B ARID bound to compound A-1 (5-(hex-1-yn-1-yl)pyridine-3-ca... -

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Basic information

Entry
Database: PDB / ID: 9ybs
TitleARID1B ARID bound to compound A-1 (5-(hex-1-yn-1-yl)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
: / AT-rich interactive domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHolliday, M.J. / Carbone, C.E.
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.
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)13,7252
Polymers13,5211
Non-polymers2031
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-1 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.728, 68.728, 45.661
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-A1CT6 / 5-(hex-1-yn-1-yl)pyridine-3-carboxylic acid


Mass: 203.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.49→59.52 Å / Num. obs: 16743 / % possible obs: 83.18 % / Redundancy: 7.37 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.015 / Net I/σ(I): 23.2
Reflection shellResolution: 1.49→1.55 Å / Redundancy: 1.44 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 455 / CC1/2: 0.935 / % possible all: 22.81

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→36.23 Å / SU ML: 0.1208 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.5206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2023 829 4.97 %
Rwork0.1697 15844 -
obs0.1712 16673 82.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.92 Å2
Refinement stepCycle: LAST / Resolution: 1.49→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 15 110 1010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062950
X-RAY DIFFRACTIONf_angle_d0.83991277
X-RAY DIFFRACTIONf_chiral_restr0.0692131
X-RAY DIFFRACTIONf_plane_restr0.0065162
X-RAY DIFFRACTIONf_dihedral_angle_d15.5744369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.590.2118650.20641050X-RAY DIFFRACTION33.54
1.59-1.710.2221410.17232602X-RAY DIFFRACTION82.62
1.71-1.880.24961920.2163018X-RAY DIFFRACTION96.14
1.88-2.150.18891210.17692942X-RAY DIFFRACTION92.99
2.15-2.710.21031450.17063103X-RAY DIFFRACTION96.67
2.71-36.230.18561650.15353129X-RAY DIFFRACTION96.6
Refinement TLS params.Method: refined / Origin x: -22.2498238511 Å / Origin y: 18.4726797611 Å / Origin z: -1.56404257095 Å
111213212223313233
T0.087491422349 Å2-0.00792103345029 Å20.00721018232258 Å2-0.101413725852 Å2-0.00420250575095 Å2--0.0787973261828 Å2
L1.61310277024 °2-0.492229735542 °20.837277540135 °2-1.81447314757 °2-0.745240756791 °2--1.4154300101 °2
S0.0584883290513 Å °0.0247310895568 Å °-0.0763170466524 Å °-0.0610959172598 Å °-0.00484416205656 Å °0.021026278783 Å °0.0259557694853 Å °0.0322173520299 Å °-0.0363959412506 Å °
Refinement TLS groupSelection details: all

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