[English] 日本語
Yorodumi
- PDB-6hi8: The ATAD2 bromodomain in complex with compound 11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hi8
TitleThe ATAD2 bromodomain in complex with compound 11
ComponentsATPase family AAA domain-containing protein 2
KeywordsCYTOSOLIC PROTEIN / Bromodomain / ATAD2 / inhibitor / complex
Function / homology
Function and homology information


nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-G6W / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSledz, P. / Caflisch, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers.
Authors: Dolbois, A. / Batiste, L. / Wiedmer, L. / Dong, J. / Brutsch, M. / Huang, D. / Deerain, N.M. / Spiliotopoulos, D. / Cheng-Sanchez, I. / Laul, E. / Nevado, C. / Sledz, P. / Caflisch, A.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8693
Polymers15,4541
Non-polymers4152
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.413, 79.413, 137.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1370-

HOH

-
Components

#1: Protein ATPase family AAA domain-containing protein 2 / Bromodomain of ATAD2


Mass: 15453.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-G6W / 2-azanyl-~{N}-[5-(5-azanylpyridin-3-yl)-4-ethanoyl-1,3-thiazol-2-yl]-2-methyl-propanamide


Mass: 319.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.04 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.9→39.71 Å / Num. obs: 38218 / % possible obs: 99.8 % / Redundancy: 5.75 % / CC1/2: 0.999 / Rrim(I) all: 0.069 / Net I/σ(I): 19.33
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 5.29 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 6119 / CC1/2: 0.603 / Rrim(I) all: 1.065 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5f36

5f36


Resolution: 1.9→39.706 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.207 1999 8.04 %
Rwork0.1935 --
obs0.1946 24853 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 21 181 1269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081114
X-RAY DIFFRACTIONf_angle_d0.9871514
X-RAY DIFFRACTIONf_dihedral_angle_d8.565971
X-RAY DIFFRACTIONf_chiral_restr0.043170
X-RAY DIFFRACTIONf_plane_restr0.005200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8995-1.9470.34861340.33492542X-RAY DIFFRACTION98
1.947-1.99960.32061360.27222612X-RAY DIFFRACTION100
1.9996-2.05840.27581390.24842584X-RAY DIFFRACTION100
2.0584-2.12490.24131360.23252571X-RAY DIFFRACTION100
2.1249-2.20080.24521340.20532600X-RAY DIFFRACTION100
2.2008-2.28890.19481350.20572604X-RAY DIFFRACTION100
2.2889-2.39310.24941360.192574X-RAY DIFFRACTION100
2.3931-2.51920.19921380.19762595X-RAY DIFFRACTION100
2.5192-2.6770.26731350.19822588X-RAY DIFFRACTION100
2.677-2.88370.26571310.18932610X-RAY DIFFRACTION100
2.8837-3.17380.22571380.19342607X-RAY DIFFRACTION100
3.1738-3.63270.20761390.17862574X-RAY DIFFRACTION100
3.6327-4.57580.1851350.152592X-RAY DIFFRACTION100
4.5758-39.71070.18411480.17582593X-RAY DIFFRACTION100

+
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