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- PDB-3m56: SET7/9 Y305F in complex with TAF10-K189me2 peptide and AdoHcy -

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Basic information

Entry
Database: PDB / ID: 3m56
TitleSET7/9 Y305F in complex with TAF10-K189me2 peptide and AdoHcy
Components
  • Histone-lysine N-methyltransferase SETD7
  • TAF10-K189me2 PEPTIDE
KeywordsTRANSFERASE / TERNARY COMPLEX / SET DOMAIN / METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / TAF10 PEPTIDE / N-DIMETHYLLYSINE / Chromatin regulator / Chromosomal protein / S-adenosyl-L-methionine / Transcription / Transcription regulation
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-ADENOSYL-L-HOMOCYSTEINE / Transcription initiation factor TFIID subunit 10 / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsDel Rizzo, P.A. / Couture, J.-F. / Roiko, M.S. / Strunk, B.S. / Brunzelle, J.S. / Dirk, L.M. / Houtz, R.L. / Trievel, R.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.
Authors: Del Rizzo, P.A. / Couture, J.F. / Dirk, L.M. / Strunk, B.S. / Roiko, M.S. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: TAF10-K189me2 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6943
Polymers30,3102
Non-polymers3841
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-5 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.953, 82.953, 95.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / SET domain-containing protein 7 / ...Histone H3-K4 methyltransferase SETD7 / H3-K4-HMTase SETD7 / SET domain-containing protein 7 / SET7/9 / Lysine N-methyltransferase 7


Mass: 29027.334 Da / Num. of mol.: 1 / Fragment: UNP residues 110-366 / Mutation: Y305F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 9606 / Gene: KIAA1717, KMT7, SET7, SET9, SETD7 / Plasmid: pHIS2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide TAF10-K189me2 PEPTIDE


Mass: 1282.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12962*PLUS
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.1 M Sodium Citrate, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0093 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.65→35 Å / Num. obs: 46006 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.059 / Χ2: 1.112 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.7160.48645451.043199.1
1.71-1.787.60.37745171.1131100
1.78-1.867.90.27945601.1771100
1.86-1.967.90.18145611.1771100
1.96-2.0880.12846061.1881100
2.08-2.247.90.09345871.0971100
2.24-2.467.80.07645971.0891100
2.46-2.827.70.06346211.1731100
2.82-3.557.40.04546711.0441100
3.55-3570.03747410.981197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.91 Å33.62 Å
Translation1.91 Å33.62 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F69

2f69


Resolution: 1.65→33.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.868 / SU B: 1.645 / SU ML: 0.056 / SU R Cruickshank DPI: 0.084 / SU Rfree: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2326 5.1 %RANDOM
Rwork0.193 ---
obs0.194 45956 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.87 Å2 / Biso mean: 26.55 Å2 / Biso min: 9.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 26 270 2247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212123
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9682910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6224.24299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10715329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.7281510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211653
X-RAY DIFFRACTIONr_mcbond_it1.0791.51299
X-RAY DIFFRACTIONr_mcangle_it1.91822111
X-RAY DIFFRACTIONr_scbond_it2.5853824
X-RAY DIFFRACTIONr_scangle_it4.1474.5785
LS refinement shellResolution: 1.65→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 183 -
Rwork0.399 3129 -
all-3312 -
obs--98.72 %

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