[English] 日本語
Yorodumi
- PDB-9ybv: ARID1B ARID bound to compound A-4 (N-[(5-methylthiophen-2-yl)meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ybv
TitleARID1B ARID bound to compound A-4 (N-[(5-methylthiophen-2-yl)methyl]-7,8-dihydro-5H-pyrano[4,3-b]pyridin-3-amine)
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: 1.2 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.
History
DepositionSep 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,8292
Polymers13,5681
Non-polymers2601
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint4 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.759, 68.759, 45.712
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

-
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: 13568.325 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-A1CT9 / N-[(5-methylthiophen-2-yl)methyl]-7,8-dihydro-5H-pyrano[4,3-b]pyridin-3-amine


Mass: 260.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
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

-
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: 1.2→36.26 Å / Num. obs: 38552 / % possible obs: 99.97 % / Redundancy: 20.14 % / Biso Wilson estimate: 14.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.013 / Net I/σ(I): 27.4
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 19.06 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3844 / CC1/2: 0.859 / % possible all: 99.97

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→36.26 Å / SU ML: 0.1572 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 1996 5.18 %
Rwork0.1894 36520 -
obs0.1903 38516 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.23 Å2
Refinement stepCycle: LAST / Resolution: 1.2→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 18 121 1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061915
X-RAY DIFFRACTIONf_angle_d0.89241232
X-RAY DIFFRACTIONf_chiral_restr0.0673130
X-RAY DIFFRACTIONf_plane_restr0.0062155
X-RAY DIFFRACTIONf_dihedral_angle_d16.0669351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.39821460.39122616X-RAY DIFFRACTION99.89
1.23-1.260.35661430.30742559X-RAY DIFFRACTION99.7
1.26-1.30.26061330.23612604X-RAY DIFFRACTION99.93
1.3-1.340.27031400.23952599X-RAY DIFFRACTION99.96
1.34-1.390.26231440.24862600X-RAY DIFFRACTION99.93
1.39-1.450.24481420.20162602X-RAY DIFFRACTION99.93
1.45-1.510.21141430.18612579X-RAY DIFFRACTION100
1.51-1.590.18451450.18312635X-RAY DIFFRACTION99.96
1.59-1.690.1931410.17672590X-RAY DIFFRACTION100
1.69-1.820.21221430.17972629X-RAY DIFFRACTION100
1.82-20.19521400.1812592X-RAY DIFFRACTION100
2.01-2.290.17751440.17882644X-RAY DIFFRACTION99.96
2.3-2.890.20781440.18622620X-RAY DIFFRACTION99.96
2.89-36.260.19261480.17682651X-RAY DIFFRACTION99.11
Refinement TLS params.Method: refined / Origin x: -5.10421654413 Å / Origin y: 28.6858212675 Å / Origin z: 1.2104456903 Å
111213212223313233
T0.104776080999 Å2-0.00988945160508 Å2-0.00572473326857 Å2-0.118345322087 Å20.00858338321484 Å2--0.102102297569 Å2
L1.38180210998 °2-0.286173238958 °2-0.34058354502 °2-1.77232517331 °20.86639093662 °2--1.35632845525 °2
S0.0129505257445 Å °-0.033787906994 Å °-0.0145665475106 Å °0.020863357845 Å °0.0286292593448 Å °-0.0508347895431 Å °0.0275793932179 Å °-0.0149383112337 Å °-0.0313795147548 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more