[English] 日本語
Yorodumi
- PDB-7tab: G-925 bound to the SMARCA4 (BRG1) Bromodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tab
TitleG-925 bound to the SMARCA4 (BRG1) Bromodomain
ComponentsIsoform 4 of Transcription activator BRG1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bromodomain BRG1 SMARCA4 inhibitor / protein binding / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyHydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 2-(6-amino-5-phenylpyridazin-3-yl)phenol / Isoform 4 of Transcription activator BRG1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsTang, Y. / Poy, F. / Taylor, A.M. / Cochran, A.G. / Bellon, S.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1.
Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, ...Authors: Taylor, A.M. / Bailey, C. / Belmont, L.D. / Campbell, R. / Cantone, N. / Cote, A. / Crawford, T.D. / Cummings, R. / DeMent, K. / Duplessis, M. / Flynn, M. / Good, A.C. / Huang, H.R. / Joshi, S. / Leblanc, Y. / Murray, J. / Nasveschuk, C.G. / Neiss, A. / Poy, F. / Romero, F.A. / Sandy, P. / Tang, Y. / Tsui, V. / Zawadzke, L. / Sims 3rd, R.J. / Audia, J.E. / Bellon, S.F. / Magnuson, S.R. / Albrecht, B.K. / Cochran, A.G.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 4 of Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3682
Polymers15,1041
Non-polymers2631
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.227, 28.597, 65.740
Angle α, β, γ (deg.)90.000, 91.310, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Isoform 4 of Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 15104.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532-4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GGU / 2-(6-amino-5-phenylpyridazin-3-yl)phenol


Mass: 263.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.74 %
Description: Very thin plates that nonetheless diffract to extreme high resolution.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein in buffer: 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, at a concentration of 15.55 mg/ml (1.03 mM) Reservoir solution contains: Jeffamine ED-2001 pH 7.0 at 30%, Tris-HCl pH 8.5 at 0.1 M, 4% PEG 400
PH range: 8.2-8.8 / Temp details: 4 degree Celsius

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98011 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. obs: 38722 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Χ2: 1.036 / Net I/σ(I): 8.6 / Num. measured all: 134810
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.16-1.22.80.5733491.054186.4
1.2-1.253.40.50338981.0611100
1.25-1.313.50.37139431.0111100
1.31-1.383.60.28139161.0231100
1.38-1.463.60.20938831.0671100
1.46-1.573.60.14539161.0281100
1.57-1.733.60.11239211.002199.9
1.73-1.983.60.08939501.044199.7
1.98-2.53.60.06439321.028199.5
2.5-503.40.0540141.051198.4

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GRC

2grc


Resolution: 1.16→32.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.434 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1943 5 %RANDOM
Rwork0.1798 ---
obs0.1809 36670 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.28 Å2 / Biso mean: 13.091 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å2-0.03 Å2
2--0.19 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.16→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 20 126 1158
Biso mean--10.6 19 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121063
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.6441429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97915219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.363157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02785
LS refinement shellResolution: 1.16→1.189 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.163 114 -
Rwork0.167 2252 -
obs--81.59 %

+
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://pdbjlvh1.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