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- PDB-4j83: SET7/9 in complex with TAF10K189A peptide and AdoMet -

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Basic information

Entry
Database: PDB / ID: 4j83
TitleSET7/9 in complex with TAF10K189A peptide and AdoMet
Components
  • Histone-lysine N-methyltransferase SETD7
  • Transcription initiation factor TFIID subunit 10
KeywordsTRANSFERASE/PEPTIDE / SET domain / lysine methyltransferase / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


SAGA complex assembly / lateral mesodermal cell differentiation / heterochromatin organization / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / transcription factor TFTC complex / hepatocyte differentiation ...SAGA complex assembly / lateral mesodermal cell differentiation / heterochromatin organization / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / transcription factor TFTC complex / hepatocyte differentiation / protein-lysine N-methyltransferase activity / RNA polymerase binding / histone H3 methyltransferase activity / limb development / transcription preinitiation complex / SAGA complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / histone methyltransferase activity / regulation of RNA splicing / embryonic placenta development / somitogenesis / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / DNA-templated transcription initiation / nuclear estrogen receptor binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / multicellular organism growth / PKMTs methylate histone lysines / G1/S transition of mitotic cell cycle / p53 binding / chromatin organization / chromosome / HATs acetylate histones / response to ethanol / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / Ub-specific processing proteases / chromatin remodeling / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit ...Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain / Histone-lysine N-methyltransferase, SET / SETD7, SET domain / Histone H3 K4-specific methyltransferase SET7 N-terminal / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MORN motif / MORN repeat / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID, 23-30kDa subunit / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Single Sheet / Beta Complex / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Transcription initiation factor TFIID subunit 10 / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHorowitz, S. / Nimtz, J.S. / Trievel, R.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases.
Authors: Horowitz, S. / Dirk, L.M. / Yesselman, J.D. / Nimtz, J.S. / Adhikari, U. / Mehl, R.A. / Scheiner, S. / Houtz, R.L. / Al-Hashimi, H.M. / Trievel, R.C.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD7
B: Transcription initiation factor TFIID subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6393
Polymers30,2412
Non-polymers3981
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area11400 Å2
MethodPISA
2
A: Histone-lysine N-methyltransferase SETD7
B: Transcription initiation factor TFIID subunit 10
hetero molecules

A: Histone-lysine N-methyltransferase SETD7
B: Transcription initiation factor TFIID subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2786
Polymers60,4814
Non-polymers7972
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3020 Å2
ΔGint-11 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.475, 83.475, 95.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone-lysine N-methyltransferase SETD7 / Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET ...Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / Lysine N-methyltransferase 7 / SET domain-containing protein 7 / SET7/9


Mass: 29043.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide Transcription initiation factor TFIID subunit 10 / STAF28 / Transcription initiation factor TFIID 30 kDa subunit / TAF(II)30 / TAFII-30 / TAFII30


Mass: 1197.363 Da / Num. of mol.: 1 / Mutation: K189A / Source method: obtained synthetically / Details: Synthetically produced peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12962
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→72.29 Å / Num. all: 43001 / Num. obs: 40793
Reflection shellResolution: 1.7→1.74 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→72.29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.609 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21138 2166 5 %RANDOM
Rwork0.18806 ---
obs0.18924 40793 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.7→72.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 27 147 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022068
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9632836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41523.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.46158
X-RAY DIFFRACTIONr_chiral_restr0.1410.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211610
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 152 -
Rwork0.228 2780 -
obs--100 %

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