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- PDB-2f69: Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide -

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Basic information

Entry
Database: PDB / ID: 2f69
TitleTernary complex of SET7/9 bound to AdoHcy and a TAF10 peptide
Components
  • Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7Histone methyltransferase
  • TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-Leu
KeywordsTRANSFERASE / SET domain / protein lysine methyltransferase / enzyme-peptide-AdoHcy complex
Function / homology
Function and homology information


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 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 / RNA polymerase binding / histone H3 methyltransferase activity / SAGA complex / limb development / transcription preinitiation complex / histone methyltransferase 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 / regulation of RNA splicing / transcription factor TFIID complex / heterochromatin organization / RNA polymerase II general transcription initiation factor activity / 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 / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / multicellular organism growth / G1/S transition of mitotic cell cycle / 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 / regulation of DNA-templated transcription / nucleolus / 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 / Resolution: 1.3 Å
AuthorsCouture, J.-F. / Collazo, E. / Hauk, G. / Trievel, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for the methylation site specificity of SET7/9
Authors: Couture, J.-F. / Collazo, E. / Hauk, G. / Trievel, R.C.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_leaving_atom_flag / _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, H3 lysine-4 specific SET7
B: TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-Leu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6963
Polymers30,3122
Non-polymers3841
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-6 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.380, 83.380, 95.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1070-

HOH

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7 / Histone methyltransferase / Histone H3-K4 methyltransferase / H3-K4-HMTase / SET domain-containing protein 7 / Set9 / 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: SET7, KIAA1717 / Plasmid: pHIS2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Protein/peptide TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-Leu


Mass: 1268.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Human TAF10 peptide / References: UniProt: Q12962*PLUS
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 61.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.89-2.04 M (NH4)2SO4, 0.1 M Bis TRIS pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.96863 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 13, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.3→29.14 Å / Num. all: 94528 / Num. obs: 94528 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.26 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 9.32 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.9 / Num. unique all: 9356 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9S

1o9s


Resolution: 1.3→29.14 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.241 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17412 4731 5 %RANDOM
Rwork0.1488 ---
all0.15008 94463 --
obs0.15008 89732 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: 24.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 26 472 2498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9712826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29324.34399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.79915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6461510
X-RAY DIFFRACTIONr_chiral_restr0.1690.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.21001
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21442
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.260.2420
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7381.51303
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.61322047
X-RAY DIFFRACTIONr_scbond_it4.6143911
X-RAY DIFFRACTIONr_scangle_it6.064.5779
X-RAY DIFFRACTIONr_rigid_bond_restr2.81532214
X-RAY DIFFRACTIONr_sphericity_free11.3123490
X-RAY DIFFRACTIONr_sphericity_bonded8.44532027
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 329 -
Rwork0.26 6587 -
obs--100 %

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