[English] 日本語
Yorodumi
- PDB-5iok: Crystal structure of Taf14 YEATS domain in complex with histone H3K9cr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iok
TitleCrystal structure of Taf14 YEATS domain in complex with histone H3K9cr
Components
  • (ACE)QTAR(KCR)ST
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / crotonylation / crotonyllysine / epigenetics / reader / histone H3 / H3K9cr
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / CENP-A containing nucleosome / global genome nucleotide-excision repair / sexual sporulation resulting in formation of a cellular spore / promoter clearance from RNA polymerase II promoter / Ino80 complex / nucleosome mobilization / transcription factor TFIIF complex ...NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / CENP-A containing nucleosome / global genome nucleotide-excision repair / sexual sporulation resulting in formation of a cellular spore / promoter clearance from RNA polymerase II promoter / Ino80 complex / nucleosome mobilization / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / chromatin assembly or disassembly / replication fork protection complex / SWI/SNF complex / mediator complex / RNA polymerase II preinitiation complex assembly / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA Polymerase II Transcription Elongation / rRNA transcription / RNA Polymerase II Pre-transcription Events / transcription elongation from RNA polymerase II promoter / histone acetylation / transcription initiation from RNA polymerase II promoter / transcription by RNA polymerase II / nucleosome / chromatin remodeling / protein heterodimerization activity / regulation of transcription, DNA-templated / DNA binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Transcription initiation factor TFIID subunit 14 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsAndrews, F.H. / Kuateladze, T.G.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: The Taf14 YEATS domain is a reader of histone crotonylation.
Authors: Andrews, F.H. / Shinsky, S.A. / Shanle, E.K. / Bridgers, J.B. / Gest, A. / Tsun, I.K. / Krajewski, K. / Shi, X. / Strahl, B.D. / Kutateladze, T.G.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
C: (ACE)QTAR(KCR)ST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2794
Polymers17,0662
Non-polymers2122
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint1 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)113.095, 113.095, 26.176
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 16180.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189
#2: Protein/peptide (ACE)QTAR(KCR)ST


Mass: 885.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide is N-terminally acetylated / Source: (synth.) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P61830*PLUS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 44% PEG600 (v/v) and 0.2 M citric acid (pH 6.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→32.65 Å / Num. obs: 9584 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 24.9
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 72.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d7e
Resolution: 2.22→32.648 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 478 5.01 %
Rwork0.2101 --
obs0.2117 9546 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→32.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 14 113 1334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091286
X-RAY DIFFRACTIONf_angle_d1.231749
X-RAY DIFFRACTIONf_dihedral_angle_d14.391488
X-RAY DIFFRACTIONf_chiral_restr0.042192
X-RAY DIFFRACTIONf_plane_restr0.006230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2202-2.54140.34221510.27672819X-RAY DIFFRACTION93
2.5414-3.20140.30531600.27343072X-RAY DIFFRACTION99
3.2014-32.65120.19241670.1713177X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.6113 Å / Origin y: 13.0749 Å / Origin z: 2.021 Å
111213212223313233
T0.197 Å20.057 Å2-0.0071 Å2-0.1684 Å2-0.0443 Å2--0.2242 Å2
L2.2747 °2-2.0209 °20.4079 °2-5.2768 °2-0.5672 °2--0.9508 °2
S0.0825 Å °0.0767 Å °0.0728 Å °-0.1244 Å °-0.1344 Å °0.1835 Å °-0.0694 Å °-0.1313 Å °0.0363 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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