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- PDB-5juw: complex of Dot1l with SS148 -

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Basic information

Entry
Database: PDB / ID: 5juw
Titlecomplex of Dot1l with SS148
ComponentsHistone-lysine N-methyltransferase, H3 lysine-79 specific
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / heterochromatin formation / telomere organization / DNA damage checkpoint signaling ...histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / heterochromatin formation / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines / gene expression / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / transcription coactivator activity / intracellular membrane-bounded organelle / DNA repair / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #60 / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / 434 Repressor (Amino-terminal Domain) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...434 Repressor (Amino-terminal Domain) - #60 / Histone H3-K79 methyltransferase, metazoa / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / 434 Repressor (Amino-terminal Domain) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6NR / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å
AuthorsYu, W. / Tempel, W. / Li, Y. / Spurr, S.S. / Bayle, E.D. / Fish, P.V. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Yu, W. / Tempel, W. / Li, Y. / Spurr, S.S. / Bayle, E.D. / Fish, P.V. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Complex of Dot1l with SS148
Authors: Yu, W. / Tempel, W. / Li, Y. / Spurr, S.S. / Bayle, E.D. / Fish, P.V. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Brown, P.J.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,38924
Polymers47,9811
Non-polymers40823
Water1,11762
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.258, 153.258, 50.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-79 specific / DOT1-like protein / Histone H3-K79 methyltransferase / H3-K79-HMTase / Lysine N-methyltransferase 4


Mass: 47980.688 Da / Num. of mol.: 1 / Fragment: UNP residues 1-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L, KIAA1814, KMT4 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#3: Chemical ChemComp-6NR / (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid


Mass: 408.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 3.58 Å3/Da / Density % sol: 65.68 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.5 M ammonium sulfate, 0.1 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792912 Å / Relative weight: 1
ReflectionResolution: 2.28→47.38 Å / Num. obs: 31441 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.28-2.3612.50.9773.13834030640.8560.2871.018100
8.83-47.3810.90.02670.4642059010.0080.02799.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.8data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3uwp

3uwp


Resolution: 2.28→47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.486 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.15
Details: Difference density indicates the approximate path of the peptide backbone between residues 56 and 63 of the model. Several attempts to place the corresponding amino acid residues in a ...Details: Difference density indicates the approximate path of the peptide backbone between residues 56 and 63 of the model. Several attempts to place the corresponding amino acid residues in a plausible conformation failed. Geometric restraints for the inhibitor were prepared with GRADE. We thank John R. Walker for suggestions during model refinement.
RfactorNum. reflection% reflection
Rfree0.2153 1516 4.8 %
Rwork0.1886 --
obs0.1899 29903 99.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.07 Å2 / Biso mean: 46.253 Å2 / Biso min: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å2-0 Å2
2---0.65 Å20 Å2
3---2.11 Å2
Refinement stepCycle: final / Resolution: 2.28→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 50 62 2640
Biso mean--37.29 42.8 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192705
X-RAY DIFFRACTIONr_bond_other_d0.0020.022460
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9373694
X-RAY DIFFRACTIONr_angle_other_deg0.96735645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60623.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12415427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0781520
X-RAY DIFFRACTIONr_chiral_restr0.090.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213147
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
X-RAY DIFFRACTIONr_mcbond_it2.1163.1381307
X-RAY DIFFRACTIONr_mcbond_other2.1163.1381307
X-RAY DIFFRACTIONr_mcangle_it3.3044.6921633
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 106 -
Rwork0.243 2190 -
all-2296 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 28.1575 Å / Origin y: 58.0558 Å / Origin z: 2.3686 Å
111213212223313233
T0.0209 Å2-0.0018 Å20.0045 Å2-0.0269 Å20.0072 Å2--0.0115 Å2
L4.1516 °2-1.6432 °20.6828 °2-2.094 °2-0.2308 °2--1.03 °2
S-0.1198 Å °-0.0591 Å °0.0566 Å °0.0297 Å °0.0802 Å °0.0343 Å °0.0983 Å °-0.0763 Å °0.0396 Å °

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