[English] 日本語
Yorodumi
- PDB-8u77: Crystal structure of Taf14 in complex with Yng1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u77
TitleCrystal structure of Taf14 in complex with Yng1
Components
  • Protein YNG1
  • Transcription initiation factor TFIID subunit 14
KeywordsTRANSCRIPTION / Complex / Taf14 / Yng1 / transcription factor
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / SUMOylation of transcription cofactors / transcription factor TFIIF complex / mediator complex / Ino80 complex / SWI/SNF complex / transcription factor TFIID complex ...PI5P Regulates TP53 Acetylation / NuA3b histone acetyltransferase complex / NuA3 histone acetyltransferase complex / NuA3a histone acetyltransferase complex / SUMOylation of transcription cofactors / transcription factor TFIIF complex / mediator complex / Ino80 complex / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / RNA polymerase II preinitiation complex assembly / methylated histone binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / ING family / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, PHD-type / PHD zinc finger ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / ING family / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 14 / Protein YNG1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNguyen, M.C. / Wei, P.C. / Zhang, G.Y. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular insight into interactions between the Taf14, Yng1 and Sas3 subunits of the NuA3 complex.
Authors: Nguyen, M.C. / Rostamian, H. / Raman, A. / Wei, P. / Becht, D.C. / Erbse, A.H. / Klein, B.J. / Gilbert, T.M. / Zhang, G. / Blanco, M.A. / Strahl, B.D. / Taverna, S.D. / Kutateladze, T.G.
History
DepositionSep 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
B: Protein YNG1
C: Transcription initiation factor TFIID subunit 14
D: Protein YNG1
E: Transcription initiation factor TFIID subunit 14
F: Protein YNG1
G: Transcription initiation factor TFIID subunit 14
H: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)37,9768
Polymers37,9768
Non-polymers00
Water5,927329
1
A: Transcription initiation factor TFIID subunit 14
B: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-10 kcal/mol
Surface area5260 Å2
MethodPISA
2
C: Transcription initiation factor TFIID subunit 14
D: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area5310 Å2
MethodPISA
3
E: Transcription initiation factor TFIID subunit 14
F: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area5020 Å2
MethodPISA
4
G: Transcription initiation factor TFIID subunit 14
H: Protein YNG1


Theoretical massNumber of molelcules
Total (without water)9,4942
Polymers9,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.780, 64.610, 64.490
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
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: 8053.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35189
#2: Protein/peptide
Protein YNG1 / ING1 homolog 1


Mass: 1440.855 Da / Num. of mol.: 4 / Fragment: UNP residues 113-124 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08465
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→45.84 Å / Num. obs: 28287 / % possible obs: 99.78 % / Redundancy: 27.2 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.04643 / Rpim(I) all: 0.04643 / Rrim(I) all: 0.06566 / Net I/σ(I): 10.92
Reflection shellResolution: 1.93→2 Å / Redundancy: 26.2 % / Rmerge(I) obs: 0.1498 / Mean I/σ(I) obs: 4.36 / Num. unique obs: 2781 / CC1/2: 0.851 / Rpim(I) all: 0.1498 / Rrim(I) all: 0.2119 / % possible all: 99.64

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→45.84 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 2000 7.08 %
Rwork0.1824 --
obs0.1852 28235 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 0 329 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052583
X-RAY DIFFRACTIONf_angle_d0.823493
X-RAY DIFFRACTIONf_dihedral_angle_d5.51324
X-RAY DIFFRACTIONf_chiral_restr0.051425
X-RAY DIFFRACTIONf_plane_restr0.004438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.28641390.21281835X-RAY DIFFRACTION99
1.98-2.030.25361440.19631881X-RAY DIFFRACTION100
2.03-2.090.22571420.18721860X-RAY DIFFRACTION100
2.09-2.160.22641420.19061865X-RAY DIFFRACTION100
2.16-2.240.22541440.17661886X-RAY DIFFRACTION100
2.24-2.330.20281430.16941871X-RAY DIFFRACTION100
2.33-2.440.20041400.17441843X-RAY DIFFRACTION100
2.44-2.560.23751430.17511882X-RAY DIFFRACTION100
2.56-2.720.20881430.18211864X-RAY DIFFRACTION100
2.72-2.930.22131450.18911904X-RAY DIFFRACTION100
2.93-3.230.22941420.19011868X-RAY DIFFRACTION100
3.23-3.70.20941440.17351879X-RAY DIFFRACTION100
3.7-4.660.20531440.16191908X-RAY DIFFRACTION100
4.66-45.840.22351450.20281889X-RAY DIFFRACTION98

+
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://pdbjlvh1.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