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- PDB-1nw3: Structure of the Catalytic domain of human DOT1L, a non-SET domai... -

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Basic information

Entry
Database: PDB / ID: 1nw3
TitleStructure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase
Componentshistone methyltransferase DOT1L
KeywordsTRANSFERASE / hDot1 / histone lysine 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
ACETATE ION / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMin, J.R. / Feng, Q. / Li, Z.H. / Zhang, Y. / Xu, R.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase
Authors: Min, J. / Feng, Q. / Li, Z. / Zhang, Y. / Xu, R.M.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: histone methyltransferase DOT1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1565
Polymers47,5061
Non-polymers6504
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.800, 152.800, 50.810
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 methyltransferase DOT1L


Mass: 47506.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: dot1 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8TEK3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 71.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125-30 mg/mlprotein1drop
220 mMTris1droppH8.0
3200 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
63 mMSAM1drop
70.1 Msodium acetate1reservoir
81.3-1.9 Mammonium sulfate1reservoir
91-3 mMTCEP1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2002 / Details: Si monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 23805 / Num. obs: 22926 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18.3
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 23800 / Num. measured all: 175389

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 1810 RANDOM
Rwork0.204 --
all-23805 -
obs-22926 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 41 68 2780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00753
X-RAY DIFFRACTIONc_angle_deg1.38386
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.66
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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