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- PDB-6jn2: Crystal structure of the coiled-coil domains of human DOT1L in co... -

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Basic information

Entry
Database: PDB / ID: 6jn2
TitleCrystal structure of the coiled-coil domains of human DOT1L in complex with AF10
Components
  • Histone-lysine N-methyltransferase, H3 lysine-79 specific
  • Protein AF-10
KeywordsTRANSFERASE / hDOT1L / hAF10 / Leucine zipper / heterodimer / tetramerization
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 / nucleosome binding / telomere organization ...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 / nucleosome binding / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines / gene expression / histone binding / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / transcription coactivator activity / intracellular membrane-bounded organelle / DNA repair / chromatin binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / 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. / PHD-finger / PHD-zinc-finger like domain ...: / : / : / 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. / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein AF-10 / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsSong, X. / Wang, M. / Yang, N. / Xu, R.M.
Funding support China, 5items
OrganizationGrant numberCountry
National Science Foundation (China)31622020 China
National Science Foundation (China)31430018 China
National Science Foundation (China)31521002 China
Ministry of Science and Technology (China)2015CB856200 China
Chinese Academy of SciencesXDB08010100 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A higher-order configuration of the heterodimeric DOT1L-AF10 coiled-coil domains potentiates their leukemogenenic activity.
Authors: Song, X. / Yang, L. / Wang, M. / Gu, Y. / Ye, B. / Fan, Z. / Xu, R.M. / Yang, N.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 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: Protein AF-10
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific


Theoretical massNumber of molelcules
Total (without water)20,5772
Polymers20,5772
Non-polymers00
Water00
1
A: Protein AF-10
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific

A: Protein AF-10
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific

A: Protein AF-10
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific

A: Protein AF-10
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific


Theoretical massNumber of molelcules
Total (without water)82,3108
Polymers82,3108
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area18550 Å2
ΔGint-164 kcal/mol
Surface area35160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.813, 107.813, 114.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Protein AF-10 / ALL1-fused gene from chromosome 10 protein


Mass: 11161.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT10, AF10 / Plasmid: pRSFDUET-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55197
#2: Protein Histone-lysine N-methyltransferase, H3 lysine-79 specific / DOT1-like protein / Histone H3-K79 methyltransferase / H3-K79-HMTase / Lysine N-methyltransferase 4


Mass: 9415.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L, KIAA1814, KMT4 / Plasmid: PRSFDUET-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8TEK3, histone-lysine N-methyltransferase

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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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M SODIUM ACETATE PH 4.8, 0.3 M KSCN, 8% V/V PENTAERYTHRITOL ETHOXYLATE (3/4 EO/OH),

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 4063 / % possible obs: 98.9 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.025 / Rrim(I) all: 0.083 / Χ2: 1.028 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.6-3.7315.93920.5640.3781.036100
3.73-3.8815.83910.8380.2931.003100
3.88-4.0515.84100.9730.1881.0171000.7290.753
4.05-4.2715.83960.9940.0870.9681000.3370.348
4.27-4.5415.64150.9940.0681.1231000.2590.269
4.54-4.8915.43940.9970.0430.981000.1620.167
4.89-5.3815.24110.9980.0361.0291000.1320.137
5.38-6.15154100.9950.051.0511000.1880.195
6.15-7.7514.14300.9980.0211.0511000.0760.079
7.75-5012.94140.9980.0151.01490.40.0530.055

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.781
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3812 387 9.5 %RANDOM
Rwork0.3242 ---
obs0.3293 3667 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 293.9 Å2 / Biso mean: 191.522 Å2 / Biso min: 103.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1098 0 0 0 1098
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191110
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9881487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5955132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51626.20758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87915233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.539156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02812
LS refinement shellResolution: 3.603→3.696 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 27 -
Rwork0.538 251 -
all-278 -
obs--96.19 %

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