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- PDB-8uwp: Crystal structure of SETDB1 Tudor domain in complex with MR46747 -

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Basic information

Entry
Database: PDB / ID: 8uwp
TitleCrystal structure of SETDB1 Tudor domain in complex with MR46747
ComponentsHistone-lysine N-methyltransferase SETDB1
KeywordsTRANSFERASE / SETDB1 / epigenetics / methyllysine reader / SGC
Function / homology
Function and homology information


[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / transposable element silencing by heterochromatin formation / heterochromatin organization / 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 / transposable element silencing by heterochromatin formation / heterochromatin organization / 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-XRU / Histone-lysine N-methyltransferase SETDB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsShrestha, S. / Beldar, S. / Dong, A. / Ackloo, S. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins.
Authors: Ackloo, S. / Li, F. / Szewczyk, M. / Seitova, A. / Loppnau, P. / Zeng, H. / Xu, J. / Ahmad, S. / Arnautova, Y.A. / Baghaie, A.J. / Beldar, S. / Bolotokova, A. / Centrella, P.A. / Chau, I. / ...Authors: Ackloo, S. / Li, F. / Szewczyk, M. / Seitova, A. / Loppnau, P. / Zeng, H. / Xu, J. / Ahmad, S. / Arnautova, Y.A. / Baghaie, A.J. / Beldar, S. / Bolotokova, A. / Centrella, P.A. / Chau, I. / Clark, M.A. / Cuozzo, J.W. / Dehghani-Tafti, S. / Disch, J.S. / Dong, A. / Dumas, A. / Feng, J.A. / Ghiabi, P. / Gibson, E. / Gilmer, J. / Goldman, B. / Green, S.R. / Guie, M.A. / Guilinger, J.P. / Harms, N. / Herasymenko, O. / Houliston, S. / Hutchinson, A. / Kearnes, S. / Keefe, A.D. / Kimani, S.W. / Kramer, T. / Kutera, M. / Kwak, H.A. / Lento, C. / Li, Y. / Liu, J. / Loup, J. / Machado, R.A.C. / Mulhern, C.J. / Perveen, S. / Righetto, G.L. / Riley, P. / Shrestha, S. / Sigel, E.A. / Silva, M. / Sintchak, M.D. / Slakman, B.L. / Taylor, R.D. / Thompson, J. / Torng, W. / Underkoffler, C. / von Rechenberg, M. / Walsh, R.T. / Watson, I. / Wilson, D.J. / Wolf, E. / Yadav, M. / Yazdi, A.K. / Zhang, J. / Zhang, Y. / Santhakumar, V. / Edwards, A.M. / Barsyte-Lovejoy, D. / Schapira, M. / Brown, P.J. / Halabelian, L. / Arrowsmith, C.H.
History
DepositionNov 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jun 4, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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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
B: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,74820
Polymers52,6752
Non-polymers2,07318
Water3,549197
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A: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,34010
Polymers26,3371
Non-polymers1,0039
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase SETDB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,40810
Polymers26,3371
Non-polymers1,0719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.285, 141.700, 55.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Plasmid: PET28A-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -PRARE2
References: UniProt: Q15047, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-XRU / (3S)-N-(4-chloro-3-{[2-(diethylamino)ethyl]carbamoyl}phenyl)-3-(diethylamino)pyrrolidine-1-carboxamide


Mass: 438.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H36ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1M Tris pH 8.2, 0.2M NH4SO4, 20% PEG8000, 2mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 49143 / % possible obs: 99 % / Redundancy: 8.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.028 / Rrim(I) all: 0.082 / Χ2: 0.977 / Net I/σ(I): 7.3 / Num. measured all: 403142
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.76-1.797.70.9424220.8810.9680.3411.0020.63798.8
1.79-1.828.10.83224270.9240.980.3010.8860.63799.5
1.82-1.868.10.67524510.9460.9860.2440.7190.649100
1.86-1.98.20.54324120.9640.9910.1960.5780.68399.5
1.9-1.9480.43724410.9740.9930.160.4660.68799.7
1.94-1.987.50.34924520.9810.9950.1330.3750.72599.8
1.98-2.037.70.30824390.9810.9950.1160.330.73499.6
2.03-2.098.70.25824580.990.9970.0910.2730.79199.9
2.09-2.158.80.21324460.9930.9980.0750.2260.78499.9
2.15-2.228.80.17724560.9950.9990.0620.1870.81999.6
2.22-2.38.60.15324320.9950.9990.0540.1630.85499.9
2.3-2.398.50.1324770.9970.9990.0460.1380.88299.9
2.39-2.58.40.1124800.9970.9990.040.1170.91100
2.5-2.638.20.09424690.9980.9990.0340.10.99100
2.63-2.797.70.08124860.9970.9990.030.0861.11499.7
2.79-3.017.80.06324500.99810.0240.0681.26299
3.01-3.318.80.05525160.99910.020.0591.49499.9
3.31-3.798.60.04725150.99910.0170.051.69499.7
3.79-4.788.10.0425460.99910.0150.0431.65299.6
4.78-507.70.03823680.99910.0150.0411.43487.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASESphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→10.05 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.744 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24243 1202 2.4 %RANDOM
Rwork0.19887 ---
obs0.19999 47896 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.305 Å2
Baniso -1Baniso -2Baniso -3
1-4.11 Å20 Å2-0 Å2
2---3.04 Å20 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 1.77→10.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 121 197 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133740
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173406
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.6475083
X-RAY DIFFRACTIONr_angle_other_deg1.2611.6067864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0895450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.17821.383188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4571525
X-RAY DIFFRACTIONr_chiral_restr0.0640.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024240
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02847
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_it2.6733.1671770
X-RAY DIFFRACTIONr_mcbond_other2.6723.1651769
X-RAY DIFFRACTIONr_mcangle_it3.9044.7372230
X-RAY DIFFRACTIONr_mcangle_other3.9044.7392231
X-RAY DIFFRACTIONr_scbond_it3.3243.5051970
X-RAY DIFFRACTIONr_scbond_other3.3233.5051971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8245.1362853
X-RAY DIFFRACTIONr_long_range_B_refined6.51736.0264020
X-RAY DIFFRACTIONr_long_range_B_other6.47635.8843989
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.813 Å
RfactorNum. reflection% reflection
Rfree0.356 80 -
Rwork0.329 3299 -
obs--93.5 %

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