[English] 日本語
Yorodumi
- PDB-7td9: G-059 bound to the SMARCA4 (BRG1) Bromodomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7td9
TitleG-059 bound to the SMARCA4 (BRG1) Bromodomain
ComponentsIsoform 4 of Transcription activator BRG1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / bromodomain BRG1 SMARCA4 inhibitor / protein binding / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyHydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 4-phenyl-5H-pyridazino[4,3-b]indol-3-amine / Isoform 4 of Transcription activator BRG1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 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 30, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Isoform 4 of Transcription activator BRG1
BBB: Isoform 4 of Transcription activator BRG1
CCC: Isoform 4 of Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0946
Polymers45,3133
Non-polymers7813
Water4,125229
1
AAA: Isoform 4 of Transcription activator BRG1
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 15.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers15,1041
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Isoform 4 of Transcription activator BRG1
hetero molecules


  • defined by author
  • 15.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers15,1041
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Isoform 4 of Transcription activator BRG1
hetero molecules


  • defined by author
  • 15.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)15,3652
Polymers15,1041
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.260, 90.260, 96.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53BBB
63CCC

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILEAAAA1452 - 15647 - 119
211SERSERILEILEBBBB1452 - 15647 - 119
322LYSLYSLYSLYSAAAA1450 - 15635 - 118
422LYSLYSLYSLYSCCCC1450 - 15635 - 118
533SERSERLYSLYSBBBB1452 - 15637 - 118
633SERSERLYSLYSCCCC1452 - 15637 - 118

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

-
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.: 3
Source method: isolated from a genetically manipulated source
Details: Two N-terminus residues "GS" are vector-derived residues.
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-GJN / 4-phenyl-5H-pyridazino[4,3-b]indol-3-amine


Mass: 260.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H12N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
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 ...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, 5% v/v Ethyl acetate
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 57838 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.044 / Net I/σ(I): 9.9 / Num. measured all: 538312
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.61-1.679.40.84457411.0011100
1.67-1.739.50.62457731.0421100
1.73-1.819.50.45957531.0771100
1.81-1.919.50.3257701.0651100
1.91-2.039.50.21457591.0221100
2.03-2.199.50.14357791.0541100
2.19-2.49.40.10157841.0271100
2.4-2.759.20.157981.081100
2.75-3.4790.06658131.031100
3.47-508.60.04658681.049199.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.15 Å
Translation2.5 Å41.15 Å

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TAB

7tab


Resolution: 1.61→41.147 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.434 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.095 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2422 2933 5.079 %
Rwork0.2063 54814 -
all0.208 --
obs-57747 99.874 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.058 Å20.029 Å20 Å2
2--0.058 Å2-0 Å2
3----0.189 Å2
Refinement stepCycle: LAST / Resolution: 1.61→41.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 60 229 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122990
X-RAY DIFFRACTIONr_angle_refined_deg1.961.6784021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58822.549153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78515614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7431521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022181
X-RAY DIFFRACTIONr_nbd_refined0.2130.21388
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2181
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.210
X-RAY DIFFRACTIONr_mcbond_it2.4482.6221398
X-RAY DIFFRACTIONr_mcangle_it3.1993.9191742
X-RAY DIFFRACTIONr_scbond_it4.1163.0461592
X-RAY DIFFRACTIONr_scangle_it5.9224.3762279
X-RAY DIFFRACTIONr_lrange_it6.60635.9874799
X-RAY DIFFRACTIONr_ncsr_local_group_10.1180.053693
X-RAY DIFFRACTIONr_ncsr_local_group_20.1370.053631
X-RAY DIFFRACTIONr_ncsr_local_group_30.1360.053585
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.117950.05007
12BBBX-RAY DIFFRACTIONLocal ncs0.117950.05007
23AAAX-RAY DIFFRACTIONLocal ncs0.13690.05007
24CCCX-RAY DIFFRACTIONLocal ncs0.13690.05007
35BBBX-RAY DIFFRACTIONLocal ncs0.135980.05007
36CCCX-RAY DIFFRACTIONLocal ncs0.135980.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.61-1.6520.2021930.17440300.17542450.9360.94599.48170.163
1.652-1.6970.1962290.17439390.17541700.9420.94799.9520.16
1.697-1.7460.2141910.17238000.17439930.940.94999.94990.157
1.746-1.80.2422010.19137380.19339450.9140.93699.84790.172
1.8-1.8590.2282060.19335940.19538060.9220.93499.84240.176
1.859-1.9240.2582010.21134730.21436780.9120.92399.89120.197
1.924-1.9960.2392060.21333440.21535520.9160.92899.94370.206
1.996-2.0770.2351570.21432570.21534140.9280.9361000.209
2.077-2.170.2631560.21831220.22132790.9110.92899.96950.217
2.17-2.2750.2591740.21329650.21531420.910.92899.90450.215
2.275-2.3980.2791570.21128200.21529810.9020.9299.86580.22
2.398-2.5430.2731610.21826620.22128240.9150.9399.96460.237
2.543-2.7180.2751170.2325410.23226580.9170.9291000.261
2.718-2.9340.2471240.23123630.23224890.9270.92699.91960.264
2.934-3.2130.2471050.23121630.23222700.9210.92499.91190.27
3.213-3.5890.234960.2219730.22120720.9370.93899.85520.254
3.589-4.1390.218910.18317480.18418390.9430.9571000.219
4.139-5.0570.223630.17914910.18115540.9430.9571000.226
5.057-7.0980.253650.20911420.21212080.950.95399.91720.264
7.098-41.1470.214400.1836490.1846980.9590.96398.71060.243

+
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