[English] 日本語
Yorodumi
- PDB-4xy8: Crystal Structure of the bromodomain of BRD9 in complex with a 2-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xy8
TitleCrystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / Bromodomain / ligand / complex / Structural Genomics Consortium / SGC
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-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
6-(5-bromo-2-methoxyphenyl)-9H-purin-2-amine / BROMIDE ION / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPicaud, S. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Filippakopoulos, P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust095751/Z/11/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2015
Title: 9H-Purine Scaffold Reveals Induced-Fit Pocket Plasticity of the BRD9 Bromodomain.
Authors: Picaud, S. / Strocchia, M. / Terracciano, S. / Lauro, G. / Mendez, J. / Daniels, D.L. / Riccio, R. / Bifulco, G. / Bruno, I. / Filippakopoulos, P.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6503
Polymers14,2501
Non-polymers4002
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-1 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.716, 43.604, 40.880
Angle α, β, γ (deg.)90.000, 104.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-487-

HOH

-
Components

#1: Protein Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8 / BRD9


Mass: 14249.763 Da / Num. of mol.: 1 / Fragment: UNP residues 14-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Details (production host): pNIC28-Bsa4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 / References: UniProt: Q9H8M2
#2: Chemical ChemComp-43U / 6-(5-bromo-2-methoxyphenyl)-9H-purin-2-amine


Mass: 320.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10BrN5O
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M NaBr, 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly,

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionResolution: 1.7→19.559 Å / Num. all: 14841 / Num. obs: 14841 / % possible obs: 97.7 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.029 / Rrim(I) all: 0.09 / Rsym value: 0.086 / Net I/av σ(I): 7.4 / Net I/σ(I): 20.3 / Num. measured all: 142203
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.799.40.3377.41935220640.1150.3377.495.2
1.79-1.99.60.242.91927120040.0810.2410.196.1
1.9-2.039.60.1674.11843219130.0560.16713.697
2.03-2.199.70.11661738317940.0390.11618.597.9
2.19-2.49.70.0967.21619816740.0320.09622.298.4
2.4-2.699.70.0877.71447614970.0290.08725.298.8
2.69-3.19.70.0768.71303813440.0260.07629.199.5
3.1-3.89.60.05710.91098911470.0190.05735.199.8
3.8-5.389.50.05311.885159010.0180.05338100
5.38-19.55990.06945495030.020.0635.398.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.55 Å
Translation3.5 Å19.55 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.21data scaling
PHASER2.1.4phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.7→19.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1883 / WRfactor Rwork: 0.1458 / FOM work R set: 0.9032 / SU B: 2.657 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0898 / SU Rfree: 0.0924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 748 5 %RANDOM
Rwork0.1482 14086 --
obs0.1502 14086 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.61 Å2 / Biso mean: 15.873 Å2 / Biso min: 3.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.57 Å2
2--0.03 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.7→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 20 191 1131
Biso mean--6.78 27.17 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019978
X-RAY DIFFRACTIONr_bond_other_d0.0010.02961
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.9991316
X-RAY DIFFRACTIONr_angle_other_deg0.8283.0042217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5595116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08222.92741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84815188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.703156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_mcbond_it2.5571.57455
X-RAY DIFFRACTIONr_mcbond_other2.5581.549454
X-RAY DIFFRACTIONr_mcangle_it3.362.893568
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 43 -
Rwork0.174 972 -
all-1015 -
obs--92.44 %
Refinement TLS params.Method: refined / Origin x: 25.9548 Å / Origin y: 15.74 Å / Origin z: -10.722 Å
111213212223313233
T0.0188 Å20.0031 Å20.0088 Å2-0.0181 Å2-0.0015 Å2--0.0176 Å2
L0.7364 °2-0.4185 °20.5184 °2-0.3688 °2-0.2422 °2--0.3888 °2
S0.0074 Å °-0.02 Å °-0.0088 Å °0.0031 Å °0.011 Å °-0.0021 Å °0.0066 Å °-0.0131 Å °-0.0184 Å °

+
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