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- PDB-5ylt: Crystal structure of SET7/9 in complex with a cyproheptadine deri... -

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Basic information

Entry
Database: PDB / ID: 5ylt
TitleCrystal structure of SET7/9 in complex with a cyproheptadine derivative
ComponentsHistone-lysine N-methyltransferase SETD7
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Set domain / methyltransferase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
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 / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...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 / 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
Chem-C7N / SINEFUNGIN / Histone-lysine N-methyltransferase SETD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHirano, T. / Fujiwara, T. / Niwa, H. / Hirano, M. / Ohira, K. / Okazaki, Y. / Sato, S. / Umehara, T. / Maemoto, Y. / Ito, A. ...Hirano, T. / Fujiwara, T. / Niwa, H. / Hirano, M. / Ohira, K. / Okazaki, Y. / Sato, S. / Umehara, T. / Maemoto, Y. / Ito, A. / Yoshida, M. / Kagechika, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
The Ministry of Education, Science, Sports and Culture, Japan15K08019 Japan
The Ministry of Education, Science, Sports and Culture, Japan26670052 Japan
The Ministry of Education, Science, Sports and Culture, Japan24613007 Japan
The Ministry of Education, Science, Sports and Culture, Japan26221204 Japan
CitationJournal: ChemMedChem / Year: 2018
Title: Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine.
Authors: Hirano, T. / Fujiwara, T. / Niwa, H. / Hirano, M. / Ohira, K. / Okazaki, Y. / Sato, S. / Umehara, T. / Maemoto, Y. / Ito, A. / Yoshida, M. / Kagechika, H.
History
DepositionOct 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0446
Polymers29,0831
Non-polymers9615
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.176, 34.963, 67.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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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: 29083.244 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 / Plasmid: PX100709-08 / Production host: CELL-FREE SYNTHESIS
References: UniProt: Q8WTS6, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-C7N / 2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol


Mass: 303.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21NO
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M TRIS-HCL PH 8.5, 34% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 30706 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Rsym value: 0.107 / Net I/σ(I): 22.6
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1473 / CC1/2: 0.467 / Rpim(I) all: 0.604 / Rrim(I) all: 1.425 / Rsym value: 1.284 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AYF

5ayf


Resolution: 1.69→42.772 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 1762 5.82 %
Rwork0.1678 --
obs0.1697 30193 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→42.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 68 197 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062079
X-RAY DIFFRACTIONf_angle_d0.8852834
X-RAY DIFFRACTIONf_dihedral_angle_d16.4861228
X-RAY DIFFRACTIONf_chiral_restr0.06299
X-RAY DIFFRACTIONf_plane_restr0.005364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.71520.34641350.29682301X-RAY DIFFRACTION98
1.7152-1.7420.27081580.26782302X-RAY DIFFRACTION99
1.742-1.77060.29511290.26562281X-RAY DIFFRACTION99
1.7706-1.80110.24961470.23852294X-RAY DIFFRACTION99
1.8011-1.83390.24061050.21422415X-RAY DIFFRACTION99
1.8339-1.86920.23521240.20672287X-RAY DIFFRACTION99
1.8692-1.90730.2311430.2012309X-RAY DIFFRACTION100
1.9073-1.94880.24511310.20432369X-RAY DIFFRACTION100
1.9488-1.99410.23041460.19412274X-RAY DIFFRACTION99
1.9941-2.0440.27161660.19182291X-RAY DIFFRACTION100
2.044-2.09920.19581440.17042296X-RAY DIFFRACTION100
2.0992-2.1610.18041750.16332304X-RAY DIFFRACTION100
2.161-2.23080.18061700.15762299X-RAY DIFFRACTION100
2.2308-2.31050.20441330.15962346X-RAY DIFFRACTION100
2.3105-2.4030.18081500.15822281X-RAY DIFFRACTION100
2.403-2.51230.19981310.1682361X-RAY DIFFRACTION100
2.5123-2.64480.16841610.16662284X-RAY DIFFRACTION100
2.6448-2.81050.20621480.16722306X-RAY DIFFRACTION100
2.8105-3.02740.16571340.15732346X-RAY DIFFRACTION100
3.0274-3.3320.22761270.15192342X-RAY DIFFRACTION100
3.332-3.81380.18081570.14092311X-RAY DIFFRACTION100
3.8138-4.8040.1771660.13012308X-RAY DIFFRACTION100
4.804-42.78610.17891080.17022345X-RAY DIFFRACTION100
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)
15.56680.19460.17443.07770.10712.4307-0.09680.0183-0.15550.04390.1362-0.6061-0.10590.3831-0.02220.1426-0.0336-0.03040.17670.00120.2136-7.16167.7197-15.7994
24.6974-5.30771.82537.0824-1.37423.2949-0.25611.0794-0.1712-0.6422-0.2645-0.64030.00590.54330.34140.4502-0.13380.1110.62990.14460.6501-4.178111.1204-25.4829
32.3059-0.19040.17892.85380.47491.6652-0.0132-0.215-0.02990.2424-0.02940.29330.0771-0.17920.02220.1539-0.00990.01160.13210.01580.0924-33.5693.278-17.7545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 115 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 364 )

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