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- PDB-9cux: Crystal Structure of SETDB1 Tudor domain in complex with UNC100016 -

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Basic information

Entry
Database: PDB / ID: 9cux
TitleCrystal Structure of SETDB1 Tudor domain in complex with UNC100016
ComponentsHistone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / Tudor domain / SETDB1 / SGC
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
: / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsSilva, M. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: Potent and selective SETDB1 covalent negative allosteric modulator reduces methyltransferase activity in cells.
Authors: Uguen, M. / Shell, D.J. / Silva, M. / Deng, Y. / Li, F. / Szewczyk, M.M. / Yang, K. / Zhao, Y. / Stashko, M.A. / Norris-Drouin, J.L. / Waybright, J.M. / Beldar, S. / Rectenwald, J.M. / ...Authors: Uguen, M. / Shell, D.J. / Silva, M. / Deng, Y. / Li, F. / Szewczyk, M.M. / Yang, K. / Zhao, Y. / Stashko, M.A. / Norris-Drouin, J.L. / Waybright, J.M. / Beldar, S. / Rectenwald, J.M. / Mordant, A.L. / Webb, T.S. / Herring, L.E. / Arrowsmith, C.H. / Ackloo, S. / Gygi, S.P. / McGinty, R.K. / Barsyte-Lovejoy, D. / Liu, P. / Halabelian, L. / James, L.I. / Pearce, K.H. / Frye, S.V.
History
DepositionJul 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 22, 2025Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_entity_nonpoly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,57217
Polymers26,3371
Non-polymers1,23416
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.834, 60.663, 70.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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: 26337.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Production host: Escherichia coli (E. coli)
References: UniProt: Q15047, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 317 molecules

#2: Chemical ChemComp-A1AZ5 / (2E)-N-(4-{[6-(dimethylamino)hexyl]amino}-2-{[5-(dimethylamino)pentyl]amino}quinazolin-6-yl)but-2-enamide


Mass: 483.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H45N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% P3350, 0.1M NH4SO4, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18061 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18061 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 60159 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.054 / Χ2: 1.031 / Net I/σ(I): 11.3 / Num. measured all: 702625
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.27-1.298.50.91629680.7190.9150.3250.9741.0399.9
1.29-1.3210.50.79929490.820.9490.2550.841.083100
1.32-1.3411.30.6529530.8570.9610.1990.681.067100
1.34-1.3710.80.55329830.90.9730.1740.581.06199.9
1.37-1.411.60.45729540.9330.9820.1390.4781.021100
1.4-1.4311.20.35629750.9610.990.110.3730.975100
1.43-1.4711.80.28929920.9790.9950.0870.3020.982100
1.47-1.5111.90.23529720.9840.9960.070.2451.012100
1.51-1.5511.20.19429900.9870.9970.060.2031.093100
1.55-1.612.10.1629800.9920.9980.0470.1671.08199.9
1.6-1.6611.50.13629860.9930.9980.0410.1421.137100
1.66-1.7212.30.11129860.9960.9990.0330.1161.113100
1.72-1.812.40.09129960.9970.9990.0270.0951.109100
1.8-1.912.10.07430180.9980.9990.0220.0771.134100
1.9-2.0212.60.06230150.99810.0180.0651.129100
2.02-2.1712.50.05130100.99910.0150.0531.056100
2.17-2.3912.70.04530300.99910.0130.0470.991100
2.39-2.7412.40.03930600.99910.0120.0410.94100
2.74-3.4512.30.0333087110.010.0340.872100
3.45-5011.70.0293255110.0090.0310.77299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→45.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.386 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18119 3050 5.1 %RANDOM
Rwork0.15892 ---
obs0.16004 57040 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0 Å2
2---1.1 Å20 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.27→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 50 301 2120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161840
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.832655
X-RAY DIFFRACTIONr_angle_other_deg0.4941.7894242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.973512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32410313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5541.3915
X-RAY DIFFRACTIONr_mcbond_other2.5471.3915
X-RAY DIFFRACTIONr_mcangle_it4.1332.3371163
X-RAY DIFFRACTIONr_mcangle_other4.1342.3391164
X-RAY DIFFRACTIONr_scbond_it2.9921.4861047
X-RAY DIFFRACTIONr_scbond_other2.9911.4871048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6242.6331493
X-RAY DIFFRACTIONr_long_range_B_refined11.88917.952313
X-RAY DIFFRACTIONr_long_range_B_other9.74215.212211
X-RAY DIFFRACTIONr_rigid_bond_restr1.76833802
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.27→1.302 Å
RfactorNum. reflection% reflection
Rfree0.511 227 -
Rwork0.456 4053 -
obs--97.41 %

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