[English] 日本語
Yorodumi
- PDB-6v1e: Crystal structure of the bromodomain of human BRD7 bound to BI7273 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v1e
TitleCrystal structure of the bromodomain of human BRD7 bound to BI7273
ComponentsBromodomain-containing protein 7
KeywordsGENE REGULATION / BRD4 / BRD / inhibitor / BI7273
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / 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 ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / 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 / regulation of mitotic cell cycle / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / lysine-acetylated histone binding / Wnt signaling pathway / kinetochore / 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 / chromatin / regulation of transcription by RNA polymerase II / 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-5SW / Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChan, A. / Karim, M.R. / 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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0093
Polymers14,5941
Non-polymers4152
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.730, 108.490, 36.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-434-

HOH

-
Components

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


Mass: 14593.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD7, BP75, CELTIX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q9NPI1
#2: Chemical ChemComp-5SW / 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one


Mass: 353.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→54.245 Å / Num. obs: 6585 / % possible obs: 99.9 % / Redundancy: 5.952 % / Biso Wilson estimate: 27.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 0.932 / Net I/σ(I): 20.58 / Num. measured all: 39195
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.366.0560.3325.7429074804800.9480.364100
2.36-2.426.0480.2946.5528734754750.9650.322100
2.42-2.56.1150.2447.427214454450.9660.267100
2.5-2.576.0820.1899.4126704404390.9850.20799.8
2.57-2.666.0210.16710.6425654264260.9850.183100
2.66-2.756.1180.14412.0625454164160.9880.158100
2.75-2.856.0280.11613.8924053993990.9940.128100
2.85-2.976.0550.11114.7923253843840.9940.121100
2.97-3.15.9760.0917.4322413753750.9970.099100
3.1-3.256.0990.0722.3521533533530.9970.076100
3.25-3.435.9970.05527.219733293290.9980.06100
3.43-3.645.8960.04232.4619223263260.9990.046100
3.64-3.895.9370.03936.2117873013010.9990.043100
3.89-4.25.8710.03840.116792872860.9990.04299.7
4.2-4.65.8560.03839.0415402632630.9990.042100
4.6-5.145.7210.03736.8314132472470.9990.041100
5.14-5.945.7660.0436.7112342142140.9980.044100
5.94-7.275.5190.03637.5310431901890.9990.03999.5
7.27-10.295.3220.02844.567611431430.9990.032100
10.29-54.2454.6110.02646.9643898950.9980.02996.9

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1-2575_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PPA

6ppa


Resolution: 2.3→54.245 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.37
RfactorNum. reflection% reflection
Rfree0.2494 330 5.01 %
Rwork0.2079 --
obs0.21 6584 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 32.9667 Å2 / Biso min: 15.58 Å2
Refinement stepCycle: final / Resolution: 2.3→54.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 30 34 1038
Biso mean--33.53 30.72 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031038
X-RAY DIFFRACTIONf_angle_d0.5521395
X-RAY DIFFRACTIONf_chiral_restr0.037146
X-RAY DIFFRACTIONf_plane_restr0.005176
X-RAY DIFFRACTIONf_dihedral_angle_d3.537906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3004-2.89830.29631610.22913053
2.8983-54.2450.23031690.19923201
Refinement TLS params.

Method: refined / 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)
12.26991.3996-0.06181.8925-0.12350.71150.2832-0.53720.65250.1158-0.01010.2992-0.0329-0.0526-0.16520.24710.04570.08790.2634-0.04830.21314.547642.112322.3258
26.29171.5675-2.24563.0307-0.17521.2583-0.05530.5320.5976-0.16970.23350.1796-0.1133-0.2706-0.140.28460.0305-0.01910.23510.03390.1516.970239.43113.1698
32.53011.57820.86693.70592.13631.23240.0338-0.06420.5133-0.7104-0.4434-0.3406-0.03270.75450.14820.25670.02640.06970.3779-0.08670.285336.455937.531117.4181
45.96512.783-2.07632.5058-0.33191.9436-0.0375-0.5105-0.14450.0327-0.0607-0.05070.152-0.04370.11430.26140.0165-0.0180.25980.00090.122411.616329.313222.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 165 )A132 - 165
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 210 )A166 - 210
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 215 )A211 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 250 )A216 - 250

+
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