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- PDB-9ybr: Binding Sites in the ARID1B DNA Binding Domain -

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Basic information

Entry
Database: PDB / ID: 9ybr
TitleBinding Sites in the ARID1B DNA Binding Domain
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: 1.45 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)13,5832
Polymers13,5211
Non-polymers621
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.835, 68.835, 46.006
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.14 %
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: 0.953725 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 1.45→36.42 Å / Num. obs: 22134 / % possible obs: 100 % / Redundancy: 20.35 % / Biso Wilson estimate: 17.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Net I/σ(I): 18.6
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 19.11 % / Rmerge(I) obs: 1.503 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2198 / CC1/2: 0.814 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→34.42 Å / SU ML: 0.1451 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.161 1983 8.97 %
Rwork0.1506 20132 -
obs0.1515 22115 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.19 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 4 99 995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085914
X-RAY DIFFRACTIONf_angle_d1.01171229
X-RAY DIFFRACTIONf_chiral_restr0.0723131
X-RAY DIFFRACTIONf_plane_restr0.0095157
X-RAY DIFFRACTIONf_dihedral_angle_d12.8364354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.31161370.28721435X-RAY DIFFRACTION100
1.49-1.530.21441450.21861426X-RAY DIFFRACTION100
1.53-1.570.16691380.17831438X-RAY DIFFRACTION99.81
1.57-1.620.17521420.16521432X-RAY DIFFRACTION99.94
1.62-1.680.17971420.15451429X-RAY DIFFRACTION99.94
1.68-1.750.19641370.16651417X-RAY DIFFRACTION100
1.75-1.830.19281420.1521437X-RAY DIFFRACTION99.94
1.83-1.920.17821430.14461447X-RAY DIFFRACTION99.94
1.92-2.040.14431350.13581420X-RAY DIFFRACTION100
2.04-2.20.16121480.13371440X-RAY DIFFRACTION100
2.2-2.420.14651450.13261436X-RAY DIFFRACTION99.94
2.42-2.770.14821390.13881452X-RAY DIFFRACTION100
2.77-3.490.14611440.15151446X-RAY DIFFRACTION100
3.49-34.420.15591460.15211477X-RAY DIFFRACTION99.33
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)
11.565921261190.131420907673-0.427380492321.804196683080.6548425071532.28982240883-0.001678986806130.04890010146770.0368302912098-0.02754397372060.045089193032-0.0434366389962-0.0233809631024-0.0942554565733-0.03250992527640.143247332270.0045542432232-0.003012416906590.144916695984-0.007017141031160.160512116401-8.1195003687235.96561896783.41947054367
24.33671086399-2.78205855687-1.657279298826.169016862422.470695453614.00740338668-0.128815495004-0.171825339046-0.3629812360520.323455090070.05712142214090.1577570355680.329691842089-0.00570757343460.1174140650230.165394737317-0.0240543863896-0.01178943654240.1481444404210.01566506525840.161009804623-3.8968693487420.48893963261.90381236908
32.08540173372-0.9939348392822.589220849175.700731691910.4485777115865.29182989910.187447579110.112297127782-0.604860863108-0.0984710532121-0.0714624271458-0.02543043956630.3546982255450.10766852203-0.05854837552680.184092285102-0.0218262606229-0.02602292853370.1780999993750.002518951179770.207213287296-7.5285231892417.3297103124-6.65579075908
42.968694717920.383627995405-0.2010274932572.95245693824-0.09991103307712.64028162822-0.00816560621013-0.058900741852-0.02776716098720.08878851373780.0285759447306-0.2119613591180.01912182536110.187966119926-0.05735179532690.1244177944550.01039148131840.00353694459380.120697524689-0.008413141618280.1497209092910.19713851575927.2333347548-0.789830984687
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 1040 through 1086 )1040 - 10861 - 47
22chain 'A' and (resid 1087 through 1106 )1087 - 110648 - 67
33chain 'A' and (resid 1107 through 1115 )1107 - 111568 - 76
44chain 'A' and (resid 1116 through 1151 )1116 - 115177 - 112

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