[English] 日本語
Yorodumi
- PDB-7eie: Crystal structure of YEATS2 YEATS domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eie
TitleCrystal structure of YEATS2 YEATS domain
ComponentsYEATS domain-containing protein 2
KeywordsNUCLEAR PROTEIN / YEATS domain / Transcription / Complex / Histone modification
Function / homology
Function and homology information


modification-dependent protein binding / ATAC complex / regulation of tubulin deacetylation / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / TBP-class protein binding / histone reader activity / mitotic spindle ...modification-dependent protein binding / ATAC complex / regulation of tubulin deacetylation / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / TBP-class protein binding / histone reader activity / mitotic spindle / transcription corepressor activity / HATs acetylate histones / histone binding / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Three-helical bundle domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
YEATS domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsKikuchi, M. / Umehara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles.
Authors: Kikuchi, M. / Morita, S. / Goto, M. / Wakamori, M. / Katsura, K. / Hanada, K. / Shirouzu, M. / Umehara, T.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2Nov 29, 2023Group: 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
A: YEATS domain-containing protein 2
B: YEATS domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5993
Polymers30,5072
Non-polymers921
Water4,143230
1
A: YEATS domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)15,2531
Polymers15,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7460 Å2
MethodPISA
2
B: YEATS domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3462
Polymers15,2531
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.448, 50.840, 82.629
Angle α, β, γ (deg.)90.00, 100.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-518-

HOH

21B-587-

HOH

-
Components

#1: Protein YEATS domain-containing protein 2


Mass: 15253.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS2, KIAA1197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULM3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl buffer (pH 8.5) containing 2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 43069 / % possible obs: 100 % / Redundancy: 3.8 % / Rsym value: 0.044 / Net I/σ(I): 11.6
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 2170 / Rsym value: 0.746

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 1.67→44.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.073 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1769 4.1 %RANDOM
Rwork0.1737 ---
obs0.17487 41299 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.22 Å2
2--1.24 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.67→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 6 230 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172035
X-RAY DIFFRACTIONr_angle_refined_deg1.141.6532951
X-RAY DIFFRACTIONr_angle_other_deg1.121.5864705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65920.229131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50915376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6751522
X-RAY DIFFRACTIONr_chiral_restr0.0470.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02507
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7734.5891010
X-RAY DIFFRACTIONr_mcbond_other1.7751009
X-RAY DIFFRACTIONr_mcangle_it2.4871266
X-RAY DIFFRACTIONr_mcangle_other2.4941267
X-RAY DIFFRACTIONr_scbond_it2.0161163
X-RAY DIFFRACTIONr_scbond_other2.0151164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6581686
X-RAY DIFFRACTIONr_long_range_B_refined3.7742299
X-RAY DIFFRACTIONr_long_range_B_other3.4482245
X-RAY DIFFRACTIONr_rigid_bond_restr0.78832149
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 135 -
Rwork0.295 3012 -
obs--100 %

+
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