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

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Basic information

Entry
Database: PDB / ID: 37el
TitleCrystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with S-ADENOSYL-L-HOMOCYSTEINE
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
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesLeishmania major strain Friedlin (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 S-ADENOSYL-L-HOMOCYSTEINE
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

Downloads & links

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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)30,1935
Polymers29,6301
Non-polymers5634
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.916, 92.340, 37.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

21A-597-

HOH

31A-617-

HOH

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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, 235 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.03 Å3/Da / Density % sol: 39.42 %
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. electron density in the active site was consistent with SAH acquired from the expression host, plate 20826 E12 ...Details: 27.5% P3350, 0.1M BT 5.5, 0.2M NaCl. LemaA.18205.a.B2.PW39520 at 12.4 mg/mL. electron density in the active site was consistent with SAH acquired from the expression host, plate 20826 E12 drop 1, Puck: PSL-1301, 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: Jan 31, 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: 1.51→46.17 Å / Num. obs: 38744 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Χ2: 1.01 / Net I/σ(I): 20.8 / Num. measured all: 510737
Reflection shellResolution: 1.51→1.55 Å / % possible obs: 99.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 1.34 / Num. measured all: 31914 / Num. unique obs: 2767 / CC1/2: 0.801 / Rpim(I) all: 0.404 / Rrim(I) all: 1.402 / Χ2: 0.82 / 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: 1.51→38.36 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1836 4.75 %
Rwork0.1674 --
obs0.169 38629 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 32 231 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082153
X-RAY DIFFRACTIONf_angle_d0.9732926
X-RAY DIFFRACTIONf_dihedral_angle_d12.875799
X-RAY DIFFRACTIONf_chiral_restr0.057318
X-RAY DIFFRACTIONf_plane_restr0.01377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.3151370.26672745X-RAY DIFFRACTION100
1.55-1.60.25941620.22722767X-RAY DIFFRACTION100
1.6-1.650.26291400.21422793X-RAY DIFFRACTION100
1.65-1.710.24561380.20072792X-RAY DIFFRACTION100
1.71-1.780.23831440.20282778X-RAY DIFFRACTION100
1.78-1.860.18671360.19052798X-RAY DIFFRACTION100
1.86-1.950.2111340.17472822X-RAY DIFFRACTION100
1.95-2.080.22281180.17542837X-RAY DIFFRACTION100
2.08-2.240.20861550.16892818X-RAY DIFFRACTION100
2.24-2.460.19591420.15822847X-RAY DIFFRACTION100
2.46-2.820.20521510.16792843X-RAY DIFFRACTION100
2.82-3.550.19371310.16012914X-RAY DIFFRACTION100
3.55-38.360.16711480.14743039X-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)
10.06410.0549-0.04910.06020.00740.154-0.20930.2860.3497-0.31510.1481-0.0058-0.13760.08920.00390.2663-0.0599-0.05020.2290.05680.2614-13.957631.1296-11.9402
20.3957-0.2338-0.22620.30560.33680.3721-0.1540.0510.3176-0.15990.13790.2591-0.0676-0.0974-0.20680.26890.0041-0.08190.22220.03890.2513-33.411224.9733-7.5909
31.51340.8669-0.82840.5522-0.43810.4727-0.2397-0.5125-0.22350.152-0.0165-0.1760.06270.1332-0.15280.27770.074-0.03320.31840.01390.1565-30.901816.82169.9429
40.67190.69720.03630.7420.10680.3074-0.15790.0446-0.0582-0.12380.147-0.0429-0.0352-0.0368-0.00050.208-0.01860.0060.20240.01180.1694-28.52668.8975-7.128
50.62090.13370.23760.6287-0.19240.2916-0.15780.036-0.3473-0.11790.1299-0.52990.0920.0733-0.21260.2055-0.02390.0840.2226-0.04060.3692-11.66935.3366-6.5564
60.97940.58690.40260.43410.01240.5983-0.21460.0731-0.1412-0.08730.1506-0.152-0.0884-0.0063-0.08990.1956-0.03650.03450.1745-0.01910.2276-7.756319.0569-5.5702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 117 )
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 203 )
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 299 )

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