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- PDB-7cd9: Crystal Structure of SETDB1 tudor domain in complexed with Compound 6 -

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Basic information

Entry
Database: PDB / ID: 7cd9
TitleCrystal Structure of SETDB1 tudor domain in complexed with Compound 6
ComponentsHistone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / SETDB1 / Tudor domain / inhibitor
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / promoter-specific chromatin binding / PKMTs methylate histone lysines ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / 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 / Pre-SET domain ...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 domain / Pre-SET motif / 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 superfamily / SET domain / SET domain profile. / SET domain
Similarity search - Domain/homology
CITRIC ACID / Chem-FVR / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXiong, L. / Guo, Y. / Mao, X. / Huang, L. / Wu, C. / 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
DepositionJun 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETDB1
B: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4986
Polymers55,2272
Non-polymers1,2714
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint0 kcal/mol
Surface area21320 Å2
Unit cell
Length a, b, c (Å)56.794, 74.938, 59.329
Angle α, β, γ (deg.)90.000, 90.730, 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.: 2
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-FVR / 3-methyl-2-[[(3R,5R)-1-methyl-5-(4-phenylmethoxyphenyl)piperidin-3-yl]amino]-5H-pyrrolo[3,2-d]pyrimidin-4-one


Mass: 443.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium citrate tribasic dihydrate 20% PEG3350 PH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 64717 / % possible obs: 98.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.996 / Net I/σ(I): 30.257
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 3196 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BHD

6bhd


Resolution: 1.6→29.662 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 3233 5 %
Rwork0.1916 61461 -
obs0.1932 64694 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.98 Å2 / Biso mean: 21.0988 Å2 / Biso min: 2.23 Å2
Refinement stepCycle: final / Resolution: 1.6→29.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 160 404 4078
Biso mean--12.69 25.36 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013704
X-RAY DIFFRACTIONf_angle_d1.1145009
X-RAY DIFFRACTIONf_chiral_restr0.065525
X-RAY DIFFRACTIONf_plane_restr0.007615
X-RAY DIFFRACTIONf_dihedral_angle_d14.6522179
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.62380.27021330.2309263297
1.6238-1.64920.28071560.2154265298
1.6492-1.67620.27491540.2256263498
1.6762-1.70510.27561290.2116266498
1.7051-1.73610.24631250.2073267599
1.7361-1.76950.25081280.2086269199
1.7695-1.80560.24491260.1954263998
1.8056-1.84490.25831130.2008267597
1.8449-1.88780.21081140.2001268599
1.8878-1.9350.24931190.2029267299
1.935-1.98730.19271600.2037268399
1.9873-2.04580.22411580.1977267399
2.0458-2.11180.23521360.1962269799
2.1118-2.18720.20291190.199263596
2.1872-2.27480.25651490.1994267499
2.2748-2.37830.24971620.19732652100
2.3783-2.50360.26851290.19712710100
2.5036-2.66040.23151430.20152719100
2.6604-2.86560.20471350.1991261896
2.8656-3.15370.22331730.18712697100
3.1537-3.60940.2061430.1782707100
3.6094-4.54480.18871320.1533268898
4.5448-5.80.19211970.184268998

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