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- PDB-6in3: Crystal structure of DOT1L in complex with 18-Crown-6 -

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Basic information

Entry
Database: PDB / ID: 6in3
TitleCrystal structure of DOT1L in complex with 18-Crown-6
ComponentsHistone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
KeywordsTRANSFERASE / histone H3K79 methyltransferase
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
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsYokoyama, T. / Kosaka, Y. / Matsumoto, K. / Kitakami, R. / Nabeshima, Y. / Mizuguchi, M.
CitationJournal: To Be Published
Title: Crown Ethers as Transthyretin Amyloidogenesis Inhibitor
Authors: Yokoyama, T. / Kosaka, Y. / Matsumoto, K. / Kitakami, R. / Nabeshima, Y. / Mizuguchi, M.
History
DepositionOct 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1798
Polymers39,0501
Non-polymers1,1297
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.092, 145.092, 56.478
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 39050.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L, KIAA1814, KMT4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase
#2: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 4.39 Å3/Da / Density % sol: 72.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 22 mM acetic acid, 78 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.57 Å / Num. obs: 30363 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rpim(I) all: 0.031 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.38 Å / Rpim(I) all: 0.354

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.3→42.002 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.2134 1518 5 %
Rwork0.1869 --
obs0.1882 30358 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 69 103 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052714
X-RAY DIFFRACTIONf_angle_d0.8113680
X-RAY DIFFRACTIONf_dihedral_angle_d19.5411019
X-RAY DIFFRACTIONf_chiral_restr0.082391
X-RAY DIFFRACTIONf_plane_restr0.005466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.37460.31521340.26112539X-RAY DIFFRACTION99
2.3746-2.45950.28751390.24552634X-RAY DIFFRACTION100
2.4595-2.55790.27331360.24012594X-RAY DIFFRACTION100
2.5579-2.67430.28891370.22082599X-RAY DIFFRACTION100
2.6743-2.81530.24591370.21832604X-RAY DIFFRACTION100
2.8153-2.99160.24361380.22552627X-RAY DIFFRACTION100
2.9916-3.22250.23711390.22372631X-RAY DIFFRACTION100
3.2225-3.54670.22921380.19012622X-RAY DIFFRACTION100
3.5467-4.05950.17821380.16432628X-RAY DIFFRACTION100
4.0595-5.11320.16171400.14652657X-RAY DIFFRACTION100
5.1132-42.00870.20651420.17412705X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.4803 Å / Origin y: 53.8009 Å / Origin z: -5.4368 Å
111213212223313233
T0.2975 Å20.0242 Å20.0226 Å2-0.4637 Å20.0234 Å2--0.3749 Å2
L2.9407 °2-1.5164 °20.8515 °2-1.7585 °2-0.6037 °2--1.7842 °2
S-0.0395 Å °-0.2394 Å °-0.1337 Å °-0.0187 Å °0.0393 Å °0.1063 Å °0.194 Å °-0.4321 Å °-0.0018 Å °
Refinement TLS groupSelection details: resseq 1:350 and not resname HOH

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