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- PDB-7cjt: Crystal Structure of SETDB1 Tudor domain in complexed with (R,R)-59 -

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Basic information

Entry
Database: PDB / ID: 7cjt
TitleCrystal Structure of SETDB1 Tudor domain in complexed with (R,R)-59
ComponentsHistone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / SETDB1 / Tudor domian / inhibitor
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / heterochromatin organization / transposable element silencing by heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / heterochromatin organization / transposable element silencing by heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3 methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / PKMTs methylate histone lysines / chromosome / methylation / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : ...Histone-lysine N-methyltransferase SETDB1 / Domain of unknown function DUF5604 / Domain of unknown function (DUF5604) / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone methyltransferase, Tudor domain 1 / Histone methyltransferase, Tudor domain 2 / Histone methyltransferase Tudor domain / Histone methyltransferase Tudor domain 1 / : / : / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Tudor domain / Tudor domain / Post-SET domain / Post-SET domain profile. / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain
Similarity search - Domain/homology
Chem-G09 / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.474 Å
AuthorsGuo, Y.P. / Liang, X. / Mao, X. / Wu, C. / Luyi, H. / Yang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81930125 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structure-Guided Discovery of a Potent and Selective Cell-Active Inhibitor of SETDB1 Tudor Domain.
Authors: Guo, Y. / Mao, X. / Xiong, L. / Xia, A. / You, J. / Lin, G. / Wu, C. / Huang, L. / Wang, Y. / Yang, S.
History
DepositionJul 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
D: Histone-lysine N-methyltransferase SETDB1
A: Histone-lysine N-methyltransferase SETDB1
B: Histone-lysine N-methyltransferase SETDB1
C: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3338
Polymers110,4544
Non-polymers1,8784
Water27015
1
D: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0832
Polymers27,6141
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0832
Polymers27,6141
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0832
Polymers27,6141
Non-polymers4701
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0832
Polymers27,6141
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.335, 69.214, 110.124
Angle α, β, γ (deg.)90.000, 98.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Histone-lysine N-methyltransferase SETDB1 / ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 ...ERG-associated protein with SET domain / ESET / Histone H3-K9 methyltransferase 4 / H3-K9-HMTase 4 / Lysine N-methyltransferase 1E / SET domain bifurcated 1


Mass: 27613.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, ESET, KIAA0067, KMT1E / Production host: Escherichia coli (E. coli)
References: UniProt: Q15047, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-G09 / 2-[[(3~{R},5~{R})-1-methyl-5-(4-phenylmethoxyphenyl)piperidin-3-yl]amino]-3-prop-2-enyl-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one


Mass: 469.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H31N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1%w/v n-Octyl-B-D-glucoside 0.1 M Sodium citrate trihydrate,pH 5.5 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.47→58.4 Å / Num. obs: 29988 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 12.1
Reflection shellResolution: 2.475→2.731 Å / Num. unique obs: 1505 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BHD

6bhd


Resolution: 2.474→41.162 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 1473 4.92 %
Rwork0.2043 28485 -
obs0.2078 29958 67.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.71 Å2 / Biso min: 16.3 Å2
Refinement stepCycle: final / Resolution: 2.474→41.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6826 0 264 15 7105
Biso mean--68.49 53.38 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167174
X-RAY DIFFRACTIONf_angle_d1.5599732
X-RAY DIFFRACTIONf_chiral_restr0.0681042
X-RAY DIFFRACTIONf_plane_restr0.011192
X-RAY DIFFRACTIONf_dihedral_angle_d14.8684180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.474-2.55380.7656180.5254320
2.5538-2.64510.5016280.4033606
2.6451-2.7510.4307420.375272737
2.751-2.87610.38251080.3253205454
2.8761-3.02770.3751540.3185262369
3.0277-3.21740.35811580.2959306280
3.2174-3.46560.32891850.24361994
3.4656-3.81420.32051970.22133828100
3.8142-4.36560.23941780.17433882100
4.3656-5.49810.22311890.15613866100
5.4981-100.23592160.1777389899

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