[English] 日本語
Yorodumi
- PDB-6ekq: Crystal structure of the human BRPF1 bromodomain complexed with B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ekq
TitleCrystal structure of the human BRPF1 bromodomain complexed with BZ054 in space group C2
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B0H / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZhu, J. / Caflisch, A.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors.
Authors: Zhu, J. / Zhou, C. / Caflisch, A.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Peregrin
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2286
Polymers27,4072
Non-polymers8214
Water7,530418
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1764
Polymers13,7041
Non-polymers4723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,7041
Non-polymers3481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.208, 57.784, 70.446
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1020-

HOH

21A-1079-

HOH

31A-1125-

HOH

41A-1142-

HOH

-
Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-B0H / ~{N}-[4-[[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]methyl]-1,3-thiazol-2-yl]-2,4-dimethyl-1,3-oxazole-5-carboxamide


Mass: 348.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N4O2S
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane pH9, 10% EG, 0.15M NaNO3, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999989 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.65→43.89 Å / Num. obs: 32602 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1588 / CC1/2: 0.879 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Mantiddata reduction
ADDREFdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.65→43.886 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1816 2000 6.14 %
Rwork0.1569 --
obs0.1584 32597 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 56 418 2329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091966
X-RAY DIFFRACTIONf_angle_d1.0332655
X-RAY DIFFRACTIONf_dihedral_angle_d7.8361688
X-RAY DIFFRACTIONf_chiral_restr0.044284
X-RAY DIFFRACTIONf_plane_restr0.005347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.22661430.18822186X-RAY DIFFRACTION100
1.6913-1.7370.2371400.18422143X-RAY DIFFRACTION100
1.737-1.78810.22471430.18612187X-RAY DIFFRACTION100
1.7881-1.84590.23761420.1812178X-RAY DIFFRACTION100
1.8459-1.91180.24451440.17562199X-RAY DIFFRACTION100
1.9118-1.98840.19811430.17472186X-RAY DIFFRACTION100
1.9884-2.07890.20291420.16322171X-RAY DIFFRACTION100
2.0789-2.18850.18241420.15452180X-RAY DIFFRACTION100
2.1885-2.32560.18711420.15862180X-RAY DIFFRACTION100
2.3256-2.50510.20131440.15972191X-RAY DIFFRACTION100
2.5051-2.75720.17431430.16122195X-RAY DIFFRACTION100
2.7572-3.15610.16341430.15412185X-RAY DIFFRACTION100
3.1561-3.97590.15071440.13412199X-RAY DIFFRACTION99
3.9759-43.9020.15951450.14912217X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 30.6951 Å / Origin y: 8.3596 Å / Origin z: 19.2005 Å
111213212223313233
T0.1021 Å20.0017 Å2-0.0226 Å2-0.0974 Å20.0073 Å2--0.0921 Å2
L0.1745 °20.1959 °2-0.2491 °2-0.2614 °20.0783 °2--0.4052 °2
S0.0608 Å °-0.0764 Å °-0.0734 Å °0.0955 Å °-0.0155 Å °-0.0569 Å °-0.0438 Å °0.0715 Å °-0.0051 Å °
Refinement TLS groupSelection details: all

+
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