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- PDB-5wxh: Crystal structure of TAF3 PHD finger bound to H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 5wxh
TitleCrystal structure of TAF3 PHD finger bound to H3K4me3
Components
  • Histone H3K4me3
  • Transcription initiation factor TFIID subunit 3
KeywordsHYDROLASE / TAF3 / histone H3
Function / homology
Function and homology information


maintenance of protein location in nucleus / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation ...maintenance of protein location in nucleus / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / positive regulation of transcription initiation by RNA polymerase II / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / male germ cell nucleus / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / mRNA transcription by RNA polymerase II / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / nuclear membrane / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
Similarity search - Function
Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.297 Å
AuthorsZhao, S. / Huang, J. / Li, H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology
Authors: Zhao, S. / Yang, M. / Zhou, W. / Zhang, B. / Cheng, Z. / Huang, J. / Zhang, M. / Wang, Z. / Wang, R. / Chen, Z. / Zhu, J. / Li, H.
History
DepositionJan 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector / _software.name
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 3
C: Transcription initiation factor TFIID subunit 3
D: Histone H3K4me3
P: Histone H3K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4808
Polymers16,2194
Non-polymers2624
Water3,297183
1
A: Transcription initiation factor TFIID subunit 3
P: Histone H3K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2404
Polymers8,1092
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area4870 Å2
MethodPISA
2
C: Transcription initiation factor TFIID subunit 3
D: Histone H3K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2404
Polymers8,1092
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-3 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.244, 35.138, 38.562
Angle α, β, γ (deg.)82.960, 75.620, 73.490
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Transcription initiation factor TFIID subunit 3 / 140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription ...140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / TAFII140


Mass: 7290.298 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF3 / Plasmid: pSUMOH10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5VWG9
#2: Protein/peptide Histone H3K4me3


Mass: 818.961 Da / Num. of mol.: 2 / Mutation: K4 acetylation / Source method: obtained synthetically / Details: chemically synthesized H3K4me3 peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MES, 0.1 M imidazole, PH6.5, 15% PEGMME 550, 15% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2015 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.297→50 Å / Num. obs: 31171 / % possible obs: 95.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.87 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.3-1.324.30.5210.897193.4
1.32-1.354.30.4550.927192.6
1.35-1.374.30.3930.934192.9
1.37-1.44.30.3640.952194.3
1.4-1.434.30.3040.957192.3
1.43-1.464.30.2660.968194.9
1.46-1.54.30.2150.977194
1.5-1.544.30.1890.981195
1.54-1.594.30.1590.984194.6
1.59-1.644.30.140.987195.6
1.64-1.74.20.120.99193.9
1.7-1.764.20.0990.993197
1.76-1.844.20.0850.994195.5
1.84-1.944.10.0770.995195.3
1.94-2.065.80.080.995197.8
2.06-2.227.80.0810.996197.7
2.22-2.457.80.0740.997197.4
2.45-2.87.60.0680.997197.8
2.8-3.5370.0620.996198.8
3.53-506.30.060.995198.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.297→37.296 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.93
RfactorNum. reflection% reflection
Rfree0.1751 1509 4.84 %
Rwork0.153 --
obs0.1541 31153 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.78 Å2 / Biso mean: 22.1144 Å2 / Biso min: 10.43 Å2
Refinement stepCycle: final / Resolution: 1.297→37.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 4 183 1286
Biso mean--17.41 33.2 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051137
X-RAY DIFFRACTIONf_angle_d0.861553
X-RAY DIFFRACTIONf_chiral_restr0.087147
X-RAY DIFFRACTIONf_plane_restr0.007201
X-RAY DIFFRACTIONf_dihedral_angle_d22.36410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2972-1.33910.21631170.21912466258388
1.3391-1.3870.21081600.20732638279893
1.387-1.44250.20261460.19092637278393
1.4425-1.50810.18191400.17582660280094
1.5081-1.58770.19971440.15592707285195
1.5877-1.68710.18271310.16012704283595
1.6871-1.81740.16331280.15172700282895
1.8174-2.00030.17621250.15362774289997
2.0003-2.28970.17651380.14852744288297
2.2897-2.88460.18061420.16072800294298
2.8846-37.31110.1591380.1362814295299
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)
10.1437-0.120.01370.0779-0.00020.03170.00410.11970.0179-0.0071-0.0570.0113-0.02340.029200.1105-0.009-0.01190.18450.00450.13131.14357.338424.1638
20.3679-0.1601-0.32020.24470.27610.3794-0.11110.0686-0.14930.016-0.01020.09540.4048-0.029-0.03950.1637-0.0077-0.00050.16130.01350.145834.79231.945134.4159
30.0877-0.0729-0.08370.05470.06020.18010.0311-0.04880.0458-0.05610.01680.1022-0.08480.014400.1743-0.00330.00540.15440.01150.126834.60879.75439.3122
40.06570.0176-0.06660.0373-0.06170.10840.0008-0.16190.10080.14560.05950.0198-0.14850.1482-0.00020.1985-0.00650.02310.184-0.00310.170732.275212.063547.8376
50.0199-0.013-0.0030.0150.0030.00170.23120.0355-0.1109-0.12480.0691-0.4088-0.1220.0942-0.00010.2373-0.0438-0.01210.2369-0.03250.311944.451616.453741.2615
60.2167-0.2011-0.10090.17790.13070.0792-0.0099-0.1258-0.03350.0745-0.08190.07690.0603-0.1045-0.00580.0995-0.0029-0.0070.1534-0.01360.132816.71626.612225.0173
70.7761-0.7382-0.18091.31390.66460.8041-0.07670.0796-0.18160.1689-0.16650.39060.2709-0.118-0.22060.1781-0.01330.03630.1308-0.01360.191714.5451-7.182519.7952
80.51260.1805-0.4210.7675-0.610.9058-0.1324-0.03910.1201-0.5188-0.15810.22140.0021-0.2833-0.19730.2082-0.0123-0.01860.2355-0.09360.28314.9179-8.718.8766
90.0389-0.0123-0.02310.03150.02460.0232-0.1278-0.1621-0.15420.11930.1456-0.27610.15990.27790.00020.18530.0349-0.01090.1699-0.00850.206523.062-6.078218.5564
100.0654-0.03870.01710.0232-0.020.03560.1312-0.0049-0.087-0.0103-0.00770.23850.1903-0.4096-0.00040.2238-0.0274-0.0450.24940.0080.21725.5727.2139.6433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 855 through 868 )A855 - 868
2X-RAY DIFFRACTION2chain 'A' and (resid 869 through 881 )A869 - 881
3X-RAY DIFFRACTION3chain 'A' and (resid 882 through 897 )A882 - 897
4X-RAY DIFFRACTION4chain 'A' and (resid 898 through 911 )A898 - 911
5X-RAY DIFFRACTION5chain 'A' and (resid 912 through 917 )A912 - 917
6X-RAY DIFFRACTION6chain 'C' and (resid 855 through 868 )C855 - 868
7X-RAY DIFFRACTION7chain 'C' and (resid 869 through 902 )C869 - 902
8X-RAY DIFFRACTION8chain 'C' and (resid 903 through 914 )C903 - 914
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 7 )D1 - 7
10X-RAY DIFFRACTION10chain 'P' and (resid 1 through 7 )P1 - 7

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