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- PDB-7edp: Crystal structure of AF10-DOT1L complex -

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Basic information

Entry
Database: PDB / ID: 7edp
TitleCrystal structure of AF10-DOT1L complex
Components
  • Histone-lysine N-methyltransferase, H3 lysine-79 specific
  • Protein AF-10
KeywordsPROTEIN BINDING / complex
Function / homology
Function and homology information


[histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / histone H3K79 trimethyltransferase activity / regulation of transcription regulatory region DNA binding / regulation of receptor signaling pathway via JAK-STAT / histone H3 methyltransferase activity / histone methyltransferase activity / telomere organization / DNA damage checkpoint signaling / heterochromatin formation ...[histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / histone H3K79 trimethyltransferase activity / regulation of transcription regulatory region DNA binding / regulation of receptor signaling pathway via JAK-STAT / histone H3 methyltransferase activity / histone methyltransferase activity / telomere organization / DNA damage checkpoint signaling / heterochromatin formation / PKMTs methylate histone lysines / gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / methylation / nucleic acid binding / transcription coactivator activity / intracellular membrane-bounded organelle / DNA repair / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
MLLT10 histone lysine methyltransferase DOT1L cofactor / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, S. / Zhou, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770801 China
CitationJournal: J Leukoc Biol / Year: 2021
Title: Structural characteristics of coiled-coil regions in AF10-DOT1L and AF10-inhibitory peptide complex.
Authors: Zhou, Z. / Kang, S. / Huang, Z. / Zhou, Z. / Chen, S.
History
DepositionMar 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,7232
Polymers9,7232
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-20 kcal/mol
Surface area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.524, 37.524, 157.445
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 4715.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TEK3, [histone H3]-lysine79 N-trimethyltransferase
#2: Protein/peptide Protein AF-10


Mass: 5007.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JT35
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.19971→31.826 Å / Num. obs: 6826 / % possible obs: 95.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.043 / Rrim(I) all: 0.132 / Net I/σ(I): 22.7
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 237 / CC1/2: 0.935

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZIK

1zik


Resolution: 2.2→31.826 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 696 10.29 %
Rwork0.2213 6067 -
obs0.2261 6763 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.56 Å2 / Biso mean: 57.0047 Å2 / Biso min: 29.06 Å2
Refinement stepCycle: final / Resolution: 2.2→31.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 0 34 687
Biso mean---56.72 -
Num. residues----83
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007653
X-RAY DIFFRACTIONf_angle_d0.866873
X-RAY DIFFRACTIONf_chiral_restr0.033110
X-RAY DIFFRACTIONf_plane_restr0.003110
X-RAY DIFFRACTIONf_dihedral_angle_d17.726259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.36950.39571040.306896078
2.3695-2.60790.28511440.2722122599
2.6079-2.9850.30721430.25081243100
2.985-3.75980.28971470.22351283100
3.7598-31.8260.22871580.1891135699
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)
12.50960.43231.36948.53046.04414.521-0.0254-0.26420.16590.4335-0.43270.177-0.2062-0.93720.35230.38460.02050.01640.32830.06980.284717.2579.351463.0941
22.54830.96273.61.06782.50358.06430.05730.05020.09470.0074-0.1221-0.0715-1.03580.35390.10890.7157-0.0412-0.01720.43980.05910.31622.297412.357454.101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 610 through 649 )B610 - 649
2X-RAY DIFFRACTION2chain 'A' and (resid 754 through 796 )A754 - 796

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