[English] 日本語
Yorodumi
- PDB-5r68: XChem group deposition -- Crystal Structure of human YEATS4 in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5r68
TitleXChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e
ComponentsYEATS domain-containing protein 4
KeywordsTRANSCRIPTION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HISTONE READER / YEATS DOMAIN
Function / homology
Function and homology information


histone H3K18ac reader activity / histone H3K27ac reader activity / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...histone H3K18ac reader activity / histone H3K27ac reader activity / Activation of the TFAP2 (AP-2) family of transcription factors / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / nuclear membrane / regulation of apoptotic process / histone binding / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
(1-methylbenzotriazol-5-yl)methanol / YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.64 Å
AuthorsRaux, B. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Huber, K.V.M.
CitationJournal: To Be Published
Title: XChem group deposition
Authors: Raux, B. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Huber, K.V.M.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: YEATS domain-containing protein 4
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2509
Polymers42,6132
Non-polymers6377
Water2,180121
1
B: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5944
Polymers21,3061
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: YEATS domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6565
Polymers21,3061
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 46.810, 58.340
Angle α, β, γ (deg.)67.390, 68.460, 69.570
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI1


Mass: 21306.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Production host: Escherichia coli (E. coli) / References: UniProt: O95619
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-RYD / (1-methylbenzotriazol-5-yl)methanol


Mass: 163.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.4 Å3/Da / Density % sol: 48.67 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M tris pH 7.5, 0.15M lithium sulfate, 40% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.64→41.93 Å / Num. obs: 46555 / % possible obs: 96.1 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.08 / Rrim(I) all: 0.113 / Net I/σ(I): 8.5 / Num. measured all: 82967 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.64-1.681.80.67611534100.6140.670.9481.195.2
7.33-41.9320.03210295210.9930.0320.04527.597.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5VNA

5vna


Resolution: 1.64→41.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.096 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2329 5 %RANDOM
Rwork0.2197 ---
obs0.2212 44226 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.2 Å2 / Biso mean: 24.21 Å2 / Biso min: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.92 Å20.8 Å2
2--0.64 Å20.34 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 1.64→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 44 121 2330
Biso mean--34.05 33.33 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132289
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172131
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6793095
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5844936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5275261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6422.522115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261510
X-RAY DIFFRACTIONr_chiral_restr0.080.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
X-RAY DIFFRACTIONr_mcbond_it2.3562.3781052
X-RAY DIFFRACTIONr_mcbond_other2.3552.3781053
X-RAY DIFFRACTIONr_mcangle_it3.3353.551309
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 177 -
Rwork0.35 3229 -
all-3406 -
obs--95.11 %

+
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