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- PDB-37ep: Crystal Structure of Histone-lysine N-methyltransferase from Leis... -

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Basic information

Entry
Database: PDB / ID: 37ep
TitleCrystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with ATP
ComponentsHistone-lysine N-methyltransferase, H3 lysine-79 specific
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Histone-lysine N-methyltransferase / Leishmania major
Function / homology
Function and homology information


histone H3K79 trimethyltransferase activity / histone H3K79 methyltransferase activity / subtelomeric heterochromatin formation / DNA damage checkpoint signaling / methylation / chromosome, telomeric region / DNA repair / nucleus
Similarity search - Function
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
ADENOSINE-5'-TRIPHOSPHATE / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Crystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with ATP
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionJul 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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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)30,2986
Polymers29,6301
Non-polymers6685
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.258, 92.397, 36.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone H3-K76 methyltransferase / Histone H3-K79 methyltransferase / Histone-lysine N- ...Histone H3-K76 methyltransferase / Histone H3-K79 methyltransferase / Histone-lysine N-methyltransferase / H3 lysine-76 specific


Mass: 29630.020 Da / Num. of mol.: 1 / Fragment: E50-K299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major strain Friedlin (eukaryote)
Gene: LMJF_07_0025 / Plasmid: LemaA.18205.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QIU2

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 27.5% P3350, 0.1M BT 5.5, 0.2M NaCl. LemaA.18205.a.B2.PW39520 at 12.4 mg/mL. overnight soak in 5 mM ATP in cryo, plate 20826 E7, Puck: PSL-0614, Cryo: 33% P3350, 0.1M BT 5.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 22, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.96→46.2 Å / Num. obs: 17538 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.044 / Rrim(I) all: 0.16 / Χ2: 1.05 / Net I/σ(I): 11.3 / Num. measured all: 229404
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.907 / Num. measured all: 17283 / Num. unique obs: 1274 / CC1/2: 0.833 / Rpim(I) all: 0.533 / Rrim(I) all: 1.981 / Χ2: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→46.2 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 900 5.15 %
Rwork0.2288 --
obs0.2309 17460 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 35 58 2029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032073
X-RAY DIFFRACTIONf_angle_d0.7222834
X-RAY DIFFRACTIONf_dihedral_angle_d16.257806
X-RAY DIFFRACTIONf_chiral_restr0.055310
X-RAY DIFFRACTIONf_plane_restr0.005355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.080.45451680.39422658X-RAY DIFFRACTION100
2.08-2.240.42261490.32222743X-RAY DIFFRACTION100
2.24-2.470.33811260.27332723X-RAY DIFFRACTION100
2.47-2.830.26681540.25722735X-RAY DIFFRACTION100
2.83-3.560.23751390.21142786X-RAY DIFFRACTION100
3.56-46.20.21771640.17992915X-RAY DIFFRACTION100
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)
10.06030.03370.08630.0455-0.10910.9532-0.46050.1351.2215-0.22640.252-0.0201-0.15760.067300.5349-0.023-0.02160.50860.06090.806-21.412230.3805-11.5174
20.061-0.0164-0.01290.104-0.06210.0393-0.27890.24780.5143-0.12460.35050.2414-0.1341-0.4612-00.54540.04130.00620.56980.03040.6979-37.121718.2123-2.4208
30.18260.0593-0.15750.51420.18480.2036-0.1280.032-0.3664-0.0483-0.2181-0.0151-0.08270.23200.4426-0.015-0.04420.45980.09950.5575-27.749817.21770.5945
40.19250.26550.01740.6175-0.10480.0520.1875-0.13870.39860.00660.24390.6195-0.0694-0.06740.09290.4513-0.0489-0.02920.4476-0.00570.3162-24.86639.2802-8.3766
50.72340.5511-0.04610.5396-0.1510.05980.08420.1504-0.51970.18980.15340.73040.17040.0711-0.00010.4885-0.0256-0.06360.47920.00570.7817-32.77685.0984-4.3792
60.54350.5712-0.51580.5935-0.53430.4731-0.0739-0.044-0.5175-0.08010.2055-0.6659-0.07030.2112-0.00010.48360.0113-0.01550.5013-0.00520.6046-11.62475.2982-6.4059
70.05390.00560.02830.070.08250.1001-0.07110.3049-0.0082-0.03310.1621-0.53240.03410.0385-00.5523-0.0395-0.03610.571-0.00270.73310.85715.496-4.2213
80.01890.0444-0.04190.1105-0.0490.091-0.21740.0006-0.460.03520.219-0.4006-0.04630.16100.5046-0.00160.03250.5035-0.0990.7666-6.120417.4891-9.9717
90.44350.18580.08290.4243-0.39910.5402-0.23170.18980.07970.0188-0.13550.2824-0.0139-0.137-00.4881-0.0291-0.00410.5054-0.04030.5751-15.340422.3704-3.6098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 127 )
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 203 )
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 249 )
7X-RAY DIFFRACTION7chain 'A' and (resid 250 through 266 )
8X-RAY DIFFRACTION8chain 'A' and (resid 267 through 279 )
9X-RAY DIFFRACTION9chain 'A' and (resid 280 through 299 )

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