[English] 日本語
Yorodumi
- PDB-6v0q: Crystal structure of the bromodomain of human BRD7 bound to TG003 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v0q
TitleCrystal structure of the bromodomain of human BRD7 bound to TG003
ComponentsBromodomain-containing protein 7
KeywordsGENE REGULATION / BRD7 / BAF / PBAF / mSWI/SNF / TG003
Function / homology
Function and homology information


histone H3K14ac reader activity / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation ...histone H3K14ac reader activity / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / Regulation of TP53 Activity through Acetylation / transcription initiation-coupled chromatin remodeling / regulation of mitotic cell cycle / : / positive regulation of cell differentiation / kinetochore / Wnt signaling pathway / nuclear matrix / transcription corepressor activity / p53 binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytosol / cytoplasm
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 ...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
Chem-EAE / PHOSPHATE ION / Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
Model detailsAPO
AuthorsKarim, M.R. / Chan, A. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.
Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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 7
B: Bromodomain-containing protein 7
C: Bromodomain-containing protein 7
D: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,04715
Polymers57,5794
Non-polymers1,46811
Water8,773487
1
A: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9917
Polymers14,3951
Non-polymers5966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6442
Polymers14,3951
Non-polymers2491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7063
Polymers14,3951
Non-polymers3112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7063
Polymers14,3951
Non-polymers3112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Bromodomain-containing protein 7
D: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,69710
Polymers28,7892
Non-polymers9078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-9 kcal/mol
Surface area13630 Å2
MethodPISA
6
B: Bromodomain-containing protein 7
hetero molecules

C: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3505
Polymers28,7892
Non-polymers5613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1950 Å2
ΔGint-8 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.970, 36.780, 118.960
Angle α, β, γ (deg.)90.000, 101.768, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Bromodomain-containing protein 7 / 75 kDa bromodomain protein / Protein CELTIX-1


Mass: 14394.644 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD7, BP75, CELTIX1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q9NPI1

-
Non-polymers , 6 types, 498 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EAE / (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one


Mass: 249.329 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C13H15NO2S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M (NH4)2SO4, 0.05 M Bis-tris (pH 6.5), and 30 % Pentaerythritol ethoxylate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2018
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→37.68 Å / Num. obs: 56788 / % possible obs: 98.5 % / Redundancy: 6.728 % / Biso Wilson estimate: 27.298 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.035 / Net I/σ(I): 19.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.736.9480.2976.7941920.9690.32199.3
1.73-1.786.9610.2547.7840730.9790.27599.5
1.78-1.836.9520.2059.3740030.9860.22199.1
1.83-1.896.8780.16111.1638410.9890.17499.1
1.89-1.956.7620.13812.6837530.9910.1598.6
1.95-2.026.6470.11315.0535770.9930.12398.4
2.02-2.16.0810.09316.6733760.9940.10296.5
2.1-2.186.4560.07919.8233660.9960.08597.8
2.18-2.287.1170.07322.5332350.9960.07999.2
2.28-2.397.1140.06623.9430800.9970.07299.1
2.39-2.527.060.06225.7429370.9970.06798.6
2.52-2.676.9170.0627.0228040.9970.06499.3
2.67-2.866.7940.05628.626270.9980.0698.5
2.86-3.096.640.05229.9524400.9970.05698.7
3.09-3.386.4260.04931.5322710.9980.05398.4
3.38-3.785.9820.04632.219970.9970.0596.9
3.78-4.366.0280.04432.8717330.9980.04894.7
4.36-5.346.750.04434.8415780.9980.04899.7
5.34-7.566.6370.04634.0612300.9980.04999.4
7.56-37.685.9470.04332.656750.9970.04794.1

-
Processing

Software
NameVersionClassification
PHENIX1.12refinement
XSCALE20180409data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PPA

6ppa


Resolution: 1.69→37.68 Å / SU ML: 0.1675 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.3428
RfactorNum. reflection% reflection
Rfree0.2179 1192 2.1 %
Rwork0.1814 --
obs0.1822 56781 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.82 Å2
Refinement stepCycle: LAST / Resolution: 1.69→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3848 0 96 487 4431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684105
X-RAY DIFFRACTIONf_angle_d0.84865518
X-RAY DIFFRACTIONf_chiral_restr0.0465584
X-RAY DIFFRACTIONf_plane_restr0.005699
X-RAY DIFFRACTIONf_dihedral_angle_d21.37761647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.760.25861330.20646187X-RAY DIFFRACTION99.36
1.76-1.840.27011310.20696143X-RAY DIFFRACTION99.21
1.84-1.930.30621330.21086183X-RAY DIFFRACTION98.92
1.93-2.060.26141310.20526096X-RAY DIFFRACTION98.08
2.06-2.210.21151290.18166042X-RAY DIFFRACTION97.4
2.21-2.440.24561340.17866215X-RAY DIFFRACTION99.19
2.44-2.790.23671330.18696202X-RAY DIFFRACTION98.95
2.79-3.510.18481330.186222X-RAY DIFFRACTION98.34
3.51-37.680.1831350.16276299X-RAY DIFFRACTION97.15

+
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