[English] 日本語
Yorodumi
- PDB-7f4a: Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f4a
TitleCrystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
Components
  • Histone H3
  • Transcription initiation factor TFIID subunit 14
KeywordsNUCLEAR PROTEIN / Histone modification / Histone benzoylation / YEATS domain / protein-protein interaction
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / transcription factor TFIIF complex / Ino80 complex / mediator complex / Oxidative Stress Induced Senescence / replication fork protection complex / SWI/SNF complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / CENP-A containing nucleosome / RNA polymerase II preinitiation complex assembly / aerobic respiration / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / 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 / : / 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
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 14 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, D. / Yan, F. / Yong, C.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010303 China
National Natural Science Foundation of China (NSFC)31970576 China
CitationJournal: Nat Commun / Year: 2022
Title: Global profiling of regulatory elements in the histone benzoylation pathway.
Authors: Wang, D. / Yan, F. / Wu, P. / Ge, K. / Li, M. / Li, T. / Gao, Y. / Peng, C. / Chen, Y.
History
DepositionJun 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)16,6742
Polymers16,6742
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-1 kcal/mol
Surface area7720 Å2
Unit cell
Length a, b, c (Å)113.786, 113.786, 26.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 15637.845 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 Histone H3


Mass: 1036.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P61830
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 48% PEG 600, 0.04M citric acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13600 / % possible obs: 98.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.033 / Rrim(I) all: 0.1 / Χ2: 0.981 / Net I/σ(I): 4.9 / Num. measured all: 125173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.037.20.7335970.7940.2780.7870.98187.5
2.03-2.077.20.6616410.8240.2520.710.99194
2.07-2.117.40.6286440.8350.2380.6731.01696.4
2.11-2.1580.5756520.8790.210.6131.01896.9
2.15-2.28.70.546940.8880.190.5740.97198.9
2.2-2.259.30.5136600.9380.1750.5430.99799.8
2.25-2.319.80.4496680.9370.1510.4740.975100
2.31-2.379.90.3857060.9560.1280.4061.014100
2.37-2.449.80.3326800.9650.1110.351.019100
2.44-2.529.30.2656690.9740.0910.2811.022100
2.52-2.619.30.2346900.9720.0810.2481.012100
2.61-2.7110.10.2136820.980.0710.2251.005100
2.71-2.8410.20.1616910.9890.0530.171.045100
2.84-2.99100.1416930.9910.0470.1491.065100
2.99-3.179.80.1046730.9960.0350.111.031100
3.17-3.429.20.0836990.9960.0290.0881.027100
3.42-3.7610.20.0657050.9980.0220.0690.978100
3.76-4.31100.0556940.9980.0180.0580.906100
4.31-5.439.10.0477130.9990.0170.0490.837100
5.43-509.10.0457490.9970.0160.0480.73599.9

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D7E

5d7e


Resolution: 2→24.111 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 634 4.93 %
Rwork0.176 12225 -
obs0.1774 12859 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.9 Å2 / Biso mean: 34.8057 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 2→24.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 110 1267
Biso mean---42.17 -
Num. residues----142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.1540.24331020.2254183772
2.154-2.37060.25961360.2113247195
2.3706-2.71330.21991460.19182569100
2.7133-3.41690.22741090.17792641100
3.4169-24.1110.16751410.15262707100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07311.81261.32818.65653.29981.85030.01880.0478-0.07830.1472-0.0224-0.4582-0.20770.2658-0.03480.1413-0.0351-0.00180.19250.0360.1772-39.53419.8560.4136
25.0491-1.3544-3.24784.22761.475.87550.1941-0.28121.044-0.20110.5453-0.0584-0.2234-0.7386-0.71670.3277-0.0858-0.05140.27660.01360.6742-39.897338.27773.7199
30.63691.85790.76127.73592.75941.3944-0.27390.280.2025-0.4492-0.29090.2258-0.38470.4139-0.2070.3446-0.1966-0.06910.16040.10150.3146-41.19819.6333-1.9926
47.71421.98141.06024.6333-3.48317.2296-0.06051.2229-0.818-0.5768-0.0508-1.00120.07270.91760.08120.2551-0.05250.11540.347-0.06940.3258-38.16942.8889-7.264
52.27181.36890.87998.9863.5665.34070.4972-0.20111.12090.8511-0.72891.4104-0.2093-0.56220.28790.3137-0.05450.13450.1545-0.06070.5335-51.644518.47013.5501
64.44560.4342-0.4666.03590.03246.5706-0.03320.34691.032-0.49540.11661.2101-0.19280.1683-0.02060.3118-0.094-0.12390.16580.14320.4446-50.232515.7959-4.5016
77.25790.39941.5563.5059-2.89922.8842-0.1887-0.14391.13640.3366-0.24120.9201-0.6156-0.21570.33830.4164-0.1031-0.08010.19240.05150.5306-44.614927.96562.0485
84.70664.82311.98557.06282.44144.48770.3209-0.52110.5981-0.0672-0.53510.5644-0.3175-0.03370.15920.1797-0.04680.0520.1299-0.01520.2233-50.37349.66143.5956
96.09687.17092.09978.73911.96561.32120.6661-0.60660.19851.1864-0.80870.0832-0.0530.02950.10640.3413-0.09390.00440.25270.05230.2022-46.250210.57316.8621
106.0916-0.5408-2.05027.7336.14012.00870.040.38580.45070.00730.0874-0.6998-0.45581.76360.00460.34-0.1714-0.07160.46610.16040.3855-33.141424.44584.1169
118.65775.54552.16554.03281.74390.90010.18140.3199-0.48910.57860.0789-0.89640.01220.2695-0.13830.2314-0.0374-0.04950.20730.03630.2188-39.00157.29893.2145
124.03973.2358-0.27037.2396-1.24233.68470.49460.7566-0.8301-0.1537-0.0993-0.49550.0837-0.0791-0.33530.27360.0516-0.01530.1939-0.03310.1873-47.9276-5.8002-5.3026
130.6211-0.96821.01319.43253.62178.62040.4197-0.21570.35090.3423-0.0933-0.1776-0.05521.351-0.4840.645-0.3439-0.12250.545-0.00910.3847-34.82527.967110.5528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )A2 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 29 )A18 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 38 )A30 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 50 )A39 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 65 )A51 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 75 )A66 - 75
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 83 )A76 - 83
8X-RAY DIFFRACTION8chain 'A' and (resid 84 through 95 )A84 - 95
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 105 )A96 - 105
10X-RAY DIFFRACTION10chain 'A' and (resid 106 through 110 )A106 - 110
11X-RAY DIFFRACTION11chain 'A' and (resid 111 through 121 )A111 - 121
12X-RAY DIFFRACTION12chain 'A' and (resid 122 through 137 )A122 - 137
13X-RAY DIFFRACTION13chain 'B' and (resid 5 through 8 )B5 - 8

+
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