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- PDB-3m59: SET7/9 Y245A in complex with TAF10-K189me2 peptide and AdoHcy -

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Basic information

Entry
Database: PDB / ID: 3m59
TitleSET7/9 Y245A 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 / Nucleus / S-adenosyl-L-methionine / Transcription / Transcription regulation
Function / homology
Function and homology information


heterochromatin organization / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / transcription factor TFTC complex / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / hepatocyte differentiation ...heterochromatin organization / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / transcription factor TFTC complex / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / hepatocyte differentiation / protein-lysine N-methyltransferase activity / SAGA complex / RNA polymerase binding / limb development / histone H3 methyltransferase activity / transcription preinitiation complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / histone methyltransferase activity / regulation of RNA splicing / 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 / embryonic placenta development / regulation of DNA repair / somitogenesis / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / male germ cell nucleus / nuclear estrogen receptor binding / promoter-specific chromatin binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / G1/S transition of mitotic cell cycle / multicellular organism growth / mRNA transcription by RNA polymerase II / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / HATs acetylate histones / response to ethanol / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / Ub-specific processing proteases / chromatin remodeling / apoptotic process / DNA damage response / chromatin binding / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / 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-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 ...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-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 superfamily / SET domain / 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: 1.7 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

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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)31,16310
Polymers30,2342
Non-polymers9308
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-24 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.497, 83.497, 95.718
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

21A-464-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 28951.236 Da / Num. of mol.: 1 / Fragment: UNP residues 110-366 / Mutation: Y245A
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

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Non-polymers , 4 types, 245 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.9 M Ammonium Sulfate, 0.1 M Bis-Tris pH 6.4, 0.005 M CoCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 / Date: Aug 2, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 40597 / % possible obs: 95 % / Redundancy: 6 % / Rmerge(I) obs: 0.055 / Χ2: 1.394 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.30.52737070.911188.1
1.76-1.835.10.45741010.884197.5
1.83-1.916.10.32241210.885197.9
1.91-2.026.30.22641530.934197.7
2.02-2.146.40.14141300.99197.1
2.14-2.316.40.140941.098196.7
2.31-2.546.50.08440931.381196
2.54-2.916.50.06240621.683195.1
2.91-3.666.60.04140711.991194
3.66-406.50.03140652.707190.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å36.16 Å
Translation3.5 Å36.16 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: 1.7→36.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.872 / SU B: 1.733 / SU ML: 0.057 / SU R Cruickshank DPI: 0.092 / SU Rfree: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2034 5 %RANDOM
Rwork0.187 ---
obs0.188 40595 95.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.66 Å2 / Biso mean: 27.057 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 53 237 2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222115
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.982888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48124.08693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64115319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.261510
X-RAY DIFFRACTIONr_chiral_restr0.1190.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211622
X-RAY DIFFRACTIONr_mcbond_it1.1091.51298
X-RAY DIFFRACTIONr_mcangle_it1.99622099
X-RAY DIFFRACTIONr_scbond_it2.663817
X-RAY DIFFRACTIONr_scangle_it4.3354.5778
LS refinement shellResolution: 1.7→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 145 -
Rwork0.357 2525 -
all-2670 -
obs--85.88 %

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