[English] 日本語
Yorodumi
- PDB-8a7i: Crystal structure of BRD9 bromodomain in complex with compound EA-89 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a7i
TitleCrystal structure of BRD9 bromodomain in complex with compound EA-89
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / Bromodomain / BRD9 / inhibitor
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-L8L / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFaller, M. / Zink, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Blood Cancer J / Year: 2022
Title: BRD9 degraders as chemosensitizers in acute leukemia and multiple myeloma.
Authors: Weisberg, E. / Chowdhury, B. / Meng, C. / Case, A.E. / Ni, W. / Garg, S. / Sattler, M. / Azab, A.K. / Sun, J. / Muz, B. / Sanchez, D. / Toure, A. / Stone, R.M. / Galinsky, I. / Winer, E. / ...Authors: Weisberg, E. / Chowdhury, B. / Meng, C. / Case, A.E. / Ni, W. / Garg, S. / Sattler, M. / Azab, A.K. / Sun, J. / Muz, B. / Sanchez, D. / Toure, A. / Stone, R.M. / Galinsky, I. / Winer, E. / Gleim, S. / Gkountela, S. / Kedves, A. / Harrington, E. / Abrams, T. / Zoller, T. / Vaupel, A. / Manley, P. / Faller, M. / Chung, B. / Chen, X. / Busenhart, P. / Stephan, C. / Calkins, K. / Bonenfant, D. / Thoma, C.R. / Forrester, W. / Griffin, J.D.
History
DepositionJun 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Bromodomain-containing protein 9
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3224
Polymers26,1322
Non-polymers1,1902
Water3,387188
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6612
Polymers13,0661
Non-polymers5951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6612
Polymers13,0661
Non-polymers5951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.083, 66.386, 55.883
Angle α, β, γ (deg.)90, 105.83, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 13066.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-L8L / ~{N}-[1,1-bis(oxidanylidene)thian-4-yl]-7-[3-methyl-1-(piperidin-4-ylmethyl)indol-5-yl]-4-oxidanylidene-5-propyl-thieno[3,2-c]pyridine-2-carboxamide


Mass: 594.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H38N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 3350, 0.1M Succinic Acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→53.764 Å / Num. obs: 21364 / % possible obs: 84.54 % / Redundancy: 1.9 % / CC1/2: 1 / Rmerge(I) obs: 0.02 / Net I/σ(I): 17.55
Reflection shellResolution: 1.76→1.823 Å / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 2507 / CC1/2: 0.914

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YY6

4yy6


Resolution: 1.76→41.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 1015 -RANDOM
Rwork0.2007 ---
obs0.2023 21347 84.6 %-
Displacement parametersBiso mean: 33.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.0103 Å20 Å20.9218 Å2
2---8.1795 Å20 Å2
3---7.1692 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.76→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 82 188 1851
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091716HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822331HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d557SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1624HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion218SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1608SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion14.95
LS refinement shellResolution: 1.76→1.77 Å
RfactorNum. reflection% reflection
Rfree0.2563 23 -
Rwork0.2466 --
obs0.2472 428 100 %
Refinement TLS params.

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)
11.45150.73150.0382.0225-0.49752.4661-0.0498-0.2434-0.0175-0.24340.09530.1253-0.01750.1253-0.0455-0.0475-0.0092-0.0140.009-0.0255-0.052-3.32132.227811.111
21.5442-0.2657-0.50441.40340.22083.67420.06870.19620.0230.1962-0.0227-0.03120.023-0.0312-0.046-0.0415-0.018-0.021-0.02590.0153-0.036911.1584-3.555133.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A138 - 238
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B138 - 238
4X-RAY DIFFRACTION2{ B|* }B301

+
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