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- PDB-7s03: DNA-binding domain of human SETMAR in complex with Hsmar1 termina... -

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Basic information

Entry
Database: PDB / ID: 7s03
TitleDNA-binding domain of human SETMAR in complex with Hsmar1 terminal inverted repeat (TIR) DNA
Components
  • (Hsmar1 terminal inverted repeats) x 2
  • Histone-lysine N-methyltransferase SETMAR
KeywordsDNA BINDING PROTEIN/DNA / SETMAR / DNA-binding domain / Hsmar1 / Helix-turn-helix / HTH / Terminal inverted repeat / TIR / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / nucleic acid metabolic process / histone H3K36 dimethyltransferase activity / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing ...negative regulation of chromosome organization / mitotic DNA integrity checkpoint signaling / [histone H3]-lysine36 N-dimethyltransferase / DNA topoisomerase binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / nucleic acid metabolic process / histone H3K36 dimethyltransferase activity / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / DNA catabolic process / histone H3K4 methyltransferase activity / positive regulation of double-strand break repair via nonhomologous end joining / replication fork processing / DNA integration / double-strand break repair via nonhomologous end joining / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / endonuclease activity / methylation / Hydrolases; Acting on ester bonds / cell population proliferation / nucleolus / protein homodimerization activity / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / : / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains ...Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / : / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone-lysine N-methyltransferase SETMAR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsChen, Q. / Georgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA151367 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing.
Authors: Chen, Q. / Bates, A.M. / Hanquier, J.N. / Simpson, E. / Rusch, D.B. / Podicheti, R. / Liu, Y. / Wek, R.C. / Cornett, E.M. / Georgiadis, M.M.
History
DepositionAug 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _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 SETMAR
B: Hsmar1 terminal inverted repeats
C: Hsmar1 terminal inverted repeats


Theoretical massNumber of molelcules
Total (without water)29,3923
Polymers29,3923
Non-polymers00
Water23413
1
A: Histone-lysine N-methyltransferase SETMAR
B: Hsmar1 terminal inverted repeats
C: Hsmar1 terminal inverted repeats

A: Histone-lysine N-methyltransferase SETMAR
B: Hsmar1 terminal inverted repeats
C: Hsmar1 terminal inverted repeats


Theoretical massNumber of molelcules
Total (without water)58,7836
Polymers58,7836
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14360 Å2
ΔGint-70 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.978, 166.172, 66.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histone-lysine N-methyltransferase SETMAR / SET domain and mariner transposase fusion protein / Metnase


Mass: 13418.327 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (UNP residues 343-453) / Mutation: I359M, C381R, L423M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETMAR / Production host: Escherichia coli (E. coli)
References: UniProt: Q53H47, [histone H3]-lysine36 N-dimethyltransferase, Hydrolases; Acting on ester bonds
#2: DNA chain Hsmar1 terminal inverted repeats


Mass: 7851.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain Hsmar1 terminal inverted repeats


Mass: 8122.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M magnesium formate, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.37→27.7 Å / Num. obs: 16176 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 71.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Net I/σ(I): 21.9
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1650 / CC1/2: 0.91 / Rpim(I) all: 0.256 / Rrim(I) all: 0.528 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→27.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.235 813 5.03 %RANDOM
Rwork0.211 ---
obs0.212 16176 99.5 %-
Displacement parametersBiso mean: 82.13 Å2
Baniso -1Baniso -2Baniso -3
1--9.526 Å20 Å20 Å2
2--15.3135 Å20 Å2
3----5.7876 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.37→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms884 1060 0 13 1957
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012086HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963033HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d600SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes179HARMONIC5
X-RAY DIFFRACTIONt_it2086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion24.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion272SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1965SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.274 163 5.73 %
Rwork0.238 2681 -
all0.24 2844 -
obs--98.68 %
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)
12.53931.61680.39773.32450.0751.24630.1001-0.24390.07450.0543-0.2154-0.0703-0.22640.0740.1153-0.0977-0.01510.0655-0.03980.0103-0.07768.735220.6483-12.8291
24.7799-1.77832.91045.81991.40528.3154-0.0677-0.36280.3491-0.4525-0.07150.21070.1393-0.53590.13920.0002-0.0955-0.152-0.0323-0.07270.015617.98563.179-3.9414
31.66490.29540.69067.05370.09181.92070.047-0.0478-0.0772-0.085-0.2443-0.5442-0.29320.35920.1973-0.2111-0.09880.058-0.11470.0411-0.095122.22525.1638-10.6774
44.7753-2.91042.91046.2427-2.88148.22050.07660.31680.5442-0.2837-0.21690.19170.0924-0.2470.14030.304-0.1171-0.152-0.22180.07330.071414.938965.8474-19.4279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|330 - A|396 }
2X-RAY DIFFRACTION2{ A|397 - A|437 }
3X-RAY DIFFRACTION3{ B|1 - B|15 C|11 - C|26 }
4X-RAY DIFFRACTION4{ C|1 - C|10 B|16 - B|26 }

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