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- PDB-5xmy: Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser -

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Basic information

Entry
Database: PDB / ID: 5xmy
TitleCrystal structure of TAF3 PHD finger bound to H3K4me3Q5ser
Components
  • Histone peptide H3(1-15)K4me3Q5ser
  • Transcription initiation factor TFIID subunit 3
KeywordsTRANSCRIPTION / zinc finger
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 / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / mRNA transcription by RNA polymerase II / negative regulation of DNA-binding transcription factor activity / p53 binding / nuclear membrane / Regulation of TP53 Activity through Phosphorylation / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsZhao, S. / Zhang, B. / Li, H.
CitationJournal: to be published
Title: Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser
Authors: Zhao, S. / Zhang, B. / Li, H.
History
DepositionMay 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
P: Histone peptide H3(1-15)K4me3Q5ser
C: Transcription initiation factor TFIID subunit 3
D: Histone peptide H3(1-15)K4me3Q5ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4808
Polymers16,2194
Non-polymers2624
Water1,928107
1
A: Transcription initiation factor TFIID subunit 3
P: Histone peptide H3(1-15)K4me3Q5ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2404
Polymers8,1092
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-4 kcal/mol
Surface area4880 Å2
MethodPISA
2
C: Transcription initiation factor TFIID subunit 3
D: Histone peptide H3(1-15)K4me3Q5ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2404
Polymers8,1092
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-4 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.982, 48.096, 52.700
Angle α, β, γ (deg.)90.000, 98.160, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Fragment: PHD finger, UNP residues 853-915 / Mutation: Y856M
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 peptide H3(1-15)K4me3Q5ser


Mass: 818.961 Da / Num. of mol.: 2 / Fragment: H3 peptide 1-15 / Mutation: K4 trimethylation Q5 serotonylation / Source method: obtained synthetically / Details: chemically synthesized H3K4me3 peptide / Source: (synth.) synthetic construct (others)
#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.: 107 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
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: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Mar 17, 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: 1.699→50 Å / Num. obs: 14658 / % possible obs: 99.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.069 / Χ2: 2.233 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.7-1.735.20.8561.195199.4
1.73-1.765.20.7161.254198.9
1.76-1.795.10.6191.259198
1.79-1.835.20.5161.375199
1.83-1.875.10.4481.441199.6
1.87-1.915.10.3571.512198.8
1.91-1.965.20.2891.522198.9
1.96-2.025.20.2331.677199.7
2.02-2.075.10.1781.814198.3
2.07-2.145.20.1661.8931100
2.14-2.225.20.1352.164199.6
2.22-2.315.20.1222.188199.2
2.31-2.415.20.0972.323199.7
2.41-2.545.20.0982.597199.6
2.54-2.750.0843.027199.6
2.7-2.9150.0713.365199.7
2.91-3.24.90.0623.765199.3
3.2-3.664.70.053.522199.7
3.66-4.614.80.0433.55199.5
4.61-504.40.0463.802196.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXdev_2689refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C13

5c13


Resolution: 1.699→25.274 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.43
RfactorNum. reflection% reflection
Rfree0.2206 729 4.98 %
Rwork0.1816 --
obs0.1835 14642 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.07 Å2 / Biso mean: 43.3708 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: final / Resolution: 1.699→25.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 4 107 1215
Biso mean--39.76 47.98 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061142
X-RAY DIFFRACTIONf_angle_d0.9151560
X-RAY DIFFRACTIONf_chiral_restr0.06148
X-RAY DIFFRACTIONf_plane_restr0.006202
X-RAY DIFFRACTIONf_dihedral_angle_d18.568665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6993-1.83050.2971570.23482699285697
1.8305-2.01470.2841430.22132759290299
2.0147-2.3060.271290.20712818294799
2.306-2.90470.25731450.211428082953100
2.9047-25.2770.18291550.15292829298499
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)
10.390.1163-0.44281.0654-0.20960.6134-0.27660.60890.2630.25910.21250.0237-0.0046-0.03280.03190.2007-0.03930.00160.2390.0630.262-2.18415.672313.3828
21.0806-0.2360.03910.5247-0.71380.43720.0066-0.201-0.0495-0.2028-0.0721-0.046-0.0360.111-0.05750.26710.0019-0.00060.14650.03370.26131.1491-2.444522.0763
30.5260.15330.22020.29940.20010.6760.1656-0.1602-0.106-0.3469-0.5036-0.03730.338-0.0132-0.28640.25910.02380.04020.14150.04970.29591.2121-6.840324.19
40.1583-0.0740.11920.2466-0.06440.5363-0.0947-0.3643-0.20960.30710.12060.02190.23690.15560.00350.33540.00560.02020.30550.10510.3282-1.6937-7.090133.8662
50.0542-0.0743-0.01080.05060.04120.00670.0719-0.0991-1.2739-0.03450.3292-0.4646-0.48070.9180.00020.31550.012-0.10730.5261-0.00140.555110.91920.353932.5961
60.1156-0.32620.08021.0829-0.43251.12850.2245-0.1831-0.202-0.31180.53031.42160.3261-1.18590.03290.2185-0.022-0.0520.2890.09970.4126-7.8167-4.727624.7273
70.5076-0.74610.24741.3105-0.2290.5983-0.14610.49370.12260.1115-0.1055-0.06990.0983-0.3866-0.12670.2014-0.0390.02210.4602-0.03430.2953-16.53245.077513.7015
81.14690.07860.53950.76910.93771.1717-0.0181-0.26950.4253-0.1337-0.23890.12790.3856-0.7859-0.0850.3546-0.04970.00120.644-0.03660.231-19.25580.7845-2.4061
90.24470.2168-0.02470.18450.08160.085-0.23790.0214-0.0750.2709-0.2645-0.40180.72410.9068-0.01090.38820.05310.01640.6723-0.05620.3504-10.57830.2979-0.3018
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 890 )A869 - 890
3X-RAY DIFFRACTION3chain 'A' and (resid 891 through 897 )A891 - 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 'P' and (resid 1 through 7 )P1 - 7
7X-RAY DIFFRACTION7chain 'C' and (resid 855 through 868 )C855 - 868
8X-RAY DIFFRACTION8chain 'C' and (resid 869 through 915 )C869 - 915
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 7 )D1 - 7

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