[English] 日本語
Yorodumi
- PDB-7r0y: ATAD2 in complex with PepLite-Glu -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r0y
TitleATAD2 in complex with PepLite-Glu
ComponentsATPase family AAA domain-containing protein 2
KeywordsTRANSCRIPTION / ATAD2 / INHIBITOR / FRAGMENT / BROMODOMAIN / FRAGLITE
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. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain ...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. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-HNU / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsTurberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC57659/A27310 United Kingdom
Cancer Research UKC1362/A20263 United Kingdom
Cancer Research UKC2215/A21421 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions.
Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 11, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0327
Polymers15,4541
Non-polymers5796
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.288, 79.288, 138.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11AAA-1330-

HOH

21AAA-1465-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, adenosinetriphosphatase

-
Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HNU / (2~{S})-2-acetamido-~{N}-prop-2-enyl-pentanediamide


Mass: 227.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate / PH range: 6-7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.43→61.48 Å / Num. obs: 47816 / % possible obs: 99.5 % / Redundancy: 19.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Rrim(I) all: 0.091 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.83-61.4815.40.0543640.9980.0180.057
1.43-1.4510.32.94322010.1951.3533.252

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAI

3dai


Resolution: 1.43→61.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.058 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2135 2335 4.891 %
Rwork0.1951 45409 -
all0.196 --
obs-47744 99.34 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.162 Å20.081 Å20 Å2
2--0.162 Å2-0 Å2
3----0.526 Å2
Refinement stepCycle: LAST / Resolution: 1.43→61.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 35 230 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0121180
X-RAY DIFFRACTIONr_angle_refined_deg2.6331.6581596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5475139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34220.6182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1371514
X-RAY DIFFRACTIONr_chiral_restr0.1510.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02929
X-RAY DIFFRACTIONr_nbd_refined0.2330.2598
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3190.2172
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6390.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4980.241
X-RAY DIFFRACTIONr_mcbond_it3.0242.641544
X-RAY DIFFRACTIONr_mcangle_it4.3853.944687
X-RAY DIFFRACTIONr_scbond_it6.1923.354636
X-RAY DIFFRACTIONr_scangle_it9.0674.798909
X-RAY DIFFRACTIONr_lrange_it12.97340.771954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.4670.3321600.3183169X-RAY DIFFRACTION95.3322
1.467-1.5070.2941550.2763140X-RAY DIFFRACTION97.6586
1.507-1.5510.2681490.2683131X-RAY DIFFRACTION98.9741
1.551-1.5990.2551510.2533061X-RAY DIFFRACTION99.9378
1.599-1.6510.2671560.2252976X-RAY DIFFRACTION99.9681
1.651-1.7090.251640.2162852X-RAY DIFFRACTION100
1.709-1.7740.2661470.2232775X-RAY DIFFRACTION100
1.774-1.8460.2321250.2112700X-RAY DIFFRACTION100
1.846-1.9280.2511280.2162584X-RAY DIFFRACTION99.9631
1.928-2.0220.2251190.2062482X-RAY DIFFRACTION100
2.022-2.1320.2271360.2032332X-RAY DIFFRACTION100
2.132-2.2610.2181160.1932246X-RAY DIFFRACTION100
2.261-2.4170.21150.1942096X-RAY DIFFRACTION100
2.417-2.610.1931000.1831972X-RAY DIFFRACTION100
2.61-2.860.2151020.1781829X-RAY DIFFRACTION100
2.86-3.1970.189720.1771681X-RAY DIFFRACTION100
3.197-3.6910.191940.1631469X-RAY DIFFRACTION100
3.691-4.520.165710.1451277X-RAY DIFFRACTION100
4.52-6.3890.216440.2061032X-RAY DIFFRACTION100
6.389-61.480.246310.271605X-RAY DIFFRACTION96.3636

+
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