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- PDB-2cxy: Crystal structure of the hBAF250b AT-rich interaction domain (ARID) -

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Basic information

Entry
Database: PDB / ID: 2cxy
TitleCrystal structure of the hBAF250b AT-rich interaction domain (ARID)
ComponentsBAF250b subunit
KeywordsDNA BINDING PROTEIN / DNA-binding domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / cellular response to angiotensin / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair ...bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / cellular response to angiotensin / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / response to ischemia / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / RMTs methylate histone arginines / nervous system development / transcription coactivator activity / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / plasma membrane / cytosol
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 / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain ...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 / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsShimada, A. / Niwa, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the hBAF250b AT-rich interaction domain (ARID)
Authors: Shimada, A. / Niwa, H. / Yokoyama, S.
History
DepositionJul 1, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAF250b subunit


Theoretical massNumber of molelcules
Total (without water)13,9741
Polymers13,9741
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.870, 68.870, 46.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein BAF250b subunit / hBAF250b


Mass: 13973.688 Da / Num. of mol.: 1 / Fragment: AT-rich interaction domain (ARID)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: hBAF250b / Plasmid: PX041105-20 / Production host: Cell free synthesis / References: UniProt: Q8NFD5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: tri-sodium citrate dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9791, 0.9794, 0.9640
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 13, 2005
RadiationMonochromator: Si double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.9641
ReflectionResolution: 1.6→50 Å / Num. all: 16439 / Num. obs: 16439 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 28.2
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.34 / Num. unique all: 1152 / Rsym value: 0.346 / % possible all: 67.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→36.53 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1148253.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 772 4.9 %RANDOM
Rwork0.185 ---
all0.186 15780 --
obs0.186 15780 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.54 Å2 / ksol: 0.378512 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å2-0.07 Å20 Å2
2---1.98 Å20 Å2
3---3.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 0 119 1022
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 113 5.5 %
Rwork0.297 1941 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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