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- PDB-8fjm: Crystal Structure of the Trypanosoma brucei DOT1A histone H3K76 m... -

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Basic information

Entry
Database: PDB / ID: 8fjm
TitleCrystal Structure of the Trypanosoma brucei DOT1A histone H3K76 methyltransferase in complex with AdoHcy - P212121 space group
ComponentsHistone-lysine N-methyltransferase, H3 lysine-79 specific
KeywordsTRANSFERASE / HISTONE LYSINE METHYLTRANSFERASE / Histone-modifying enzyme / DOT1A / Trypanosoma brucei / AdoHcy complex
Function / homology
Function and homology information


histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / DNA damage checkpoint signaling / chromosome / methylation / 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
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFrisbie, V.S. / Hashimoto, H. / Debler, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI165840-01A1 United States
CitationJournal: To Be Published
Title: Structure and Mechanism of the atypical Trypanosoma brucei DOT1A histone H3K76 methyltransferase
Authors: Frisbie, V.S. / Hashimoto, H. / Xie, Y. / Baeza, J. / Nguyen, T. / Yuan, Z. / Garcia, B.A. / Debler, E.W.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: 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
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6909
Polymers58,6522
Non-polymers1,0397
Water6,359353
1
A: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8164
Polymers29,3261
Non-polymers4903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8755
Polymers29,3261
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.934, 81.625, 170.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone H3-K79 methyltransferase / DOT1A


Mass: 29325.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: Lister / Gene: Tb08.26N11.380, Tb927.8.1920 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q581Z0, [histone H3]-lysine79 N-trimethyltransferase

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Non-polymers , 5 types, 360 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG 3,000, 200 mM calcium acetate, 100 mM Tris-HCl, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→40.81 Å / Num. obs: 47091 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 20.52 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.053 / Rsym value: 0.161 / Χ2: 0.907 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4561 / CC1/2: 0.963 / CC star: 0.991 / Rpim(I) all: 0.531 / Rsym value: 1.323 / Χ2: 0.951 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.81 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1855 2796 4.75 %
Rwork0.16 56056 -
obs0.1612 42001 66.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 60 353 4334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434072
X-RAY DIFFRACTIONf_angle_d0.7495499
X-RAY DIFFRACTIONf_chiral_restr0.0438600
X-RAY DIFFRACTIONf_plane_restr0.0069707
X-RAY DIFFRACTIONf_dihedral_angle_d15.20391530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.2969490.2634985X-RAY DIFFRACTION23.47
1.93-1.970.335560.23581130X-RAY DIFFRACTION26.79
1.97-20.2699660.22591305X-RAY DIFFRACTION30.5
2-2.050.2712780.22381606X-RAY DIFFRACTION38.21
2.05-2.090.2392960.23491876X-RAY DIFFRACTION43.66
2.09-2.140.25931080.21392101X-RAY DIFFRACTION50.08
2.14-2.190.23741140.21042205X-RAY DIFFRACTION51.9
2.19-2.250.22271250.19732396X-RAY DIFFRACTION57.07
2.25-2.320.18631300.18212543X-RAY DIFFRACTION59.67
2.32-2.390.21241320.16972636X-RAY DIFFRACTION62.67
2.39-2.480.20791370.16242832X-RAY DIFFRACTION65.74
2.48-2.580.20321510.16992962X-RAY DIFFRACTION70.72
2.58-2.690.22281580.16543194X-RAY DIFFRACTION75.55
2.69-2.840.23111560.17163363X-RAY DIFFRACTION78.94
2.84-3.010.1832000.15583915X-RAY DIFFRACTION92
3.01-3.250.18961950.15284104X-RAY DIFFRACTION96.93
3.25-3.570.172080.14594232X-RAY DIFFRACTION99.62
3.57-4.090.14382090.12834197X-RAY DIFFRACTION99.46
4.09-5.150.12932180.12834254X-RAY DIFFRACTION99.91
5.15-40.810.20512100.17894220X-RAY DIFFRACTION99.75
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)
11.30255037277-0.7144378425331.759247834691.45692350415-1.070779267714.993743384070.2683599334640.30165493837-0.336225475157-0.160145200852-0.121559142412-0.003083557280180.599589249550.490297200214-0.1936851056960.2185100655180.0797209242768-0.01016080181830.179189504987-0.01966066469160.203390048692.17149181637-5.86002517666-33.1229207764
21.573444184652.879525996981.446021183288.371017403774.391299080855.35353544740.04644196568260.2419297747550.205287071934-0.3955675056590.01761895286330.113766694862-0.461357708480.0611832544721-0.0784984974980.224007367040.05713211177540.05197257203430.2205295059480.04617155078390.161905055934-5.5866607689517.6520307735-32.5084184876
32.44771871154-0.422943180474-0.5701351059254.109288567040.6807421535934.975494624540.07631839971840.1091822336460.1369415122830.1111787060670.0741595774726-0.175986405888-0.3316640668520.202474204038-0.1710874748850.1105747638260.03695066143780.004381016550340.1289820185770.01587299594670.1302705016110.01435517727697.26984234906-25.3134371456
42.180168729880.9825880363910.9061869160385.285685886741.264584618633.875779452590.0581640052751-0.0891388479952-0.0327151262669-0.103328698216-0.0754805786890.0549683933584-0.0787496326219-0.3506118042510.0004510216121040.06069553561630.02357123270660.004648044255430.1580957402650.00257460110080.112762116792-10.39249619366.7216417725-20.8079381606
51.62786373718-0.1981737244780.407618052511.53366857717-0.8014131771032.600549099060.01305344607870.07674302578160.1357845198990.03859195344050.0621663920460.18377219113-0.398789034704-0.464771322964-0.05043591388090.1945130271780.08189005687930.04300277642140.1888036304060.007462906623090.215020853638-14.291481388414.6567336414-22.9457743766
63.329966041421.00519121423-1.157297243422.63684438646-0.5506193513754.660674240670.0234321886471-0.09572372864930.1200152094560.07641138538970.05427120964660.00606695630909-0.110824260833-0.0254163205553-0.07625159663040.09811671758240.0125722624569-0.01140623485410.06818599085550.01642808985530.108974653922-3.443854282065.21631188418-8.77560177689
71.72344584381-0.966444589510.3219054440812.01168167136-1.356653062635.294321395580.07253176486810.06895411432110.1031574366680.036790638022-0.119399520853-0.1873120029770.01020397478230.452003692540.06593834057980.0888590357913-0.0144438294592-0.002560864183090.13423187984-0.003506484464840.1629513202396.96927993591-0.751834485423-15.4736008396
81.354180878420.4368313157360.2878871430042.858196635530.3148288400753.58283160915-0.1951879246610.149039994355-0.0471139865212-0.1980445208550.077446657094-0.151091462706-0.3587195700510.0630635758440.09416777203850.224797267987-0.0533430658477-0.02868712329540.1605985187940.02728730161630.1425124999718.47786051419-32.4243448478-31.4576198713
91.580952889590.1309057621661.301666275421.34912697478-0.1089005339313.38460541848-0.154910906718-0.1789396923340.07619915654290.02531696397010.03204576099780.0531646213104-0.336876705689-0.3634275017170.08500236526720.1357647238610.04241688263470.002230350390650.1554082403090.01036096645730.1485200442444.71456394676-36.3990848707-14.2035038079
101.078826672971.4160045852-1.065914397733.36637607146-0.8348889387124.67624475485-0.2537032684520.1980944787710.275631370015-0.1888573801370.2614039262960.336540939258-1.05971972592-0.329544546946-0.08385510228290.335582285932-0.0039238209013-0.06666717824160.1549881733740.02444403891410.2212892250778.3347711984-25.2222739806-22.0040077873
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 45 through 78 )AA45 - 781 - 34
22chain 'A' and (resid 79 through 104 )AA79 - 10435 - 60
33chain 'A' and (resid 105 through 123 )AA105 - 12361 - 79
44chain 'A' and (resid 124 through 160 )AA124 - 16080 - 116
55chain 'A' and (resid 161 through 200 )AA161 - 200117 - 156
66chain 'A' and (resid 201 through 245 )AA201 - 245157 - 201
77chain 'A' and (resid 246 through 295 )AA246 - 295202 - 251
88chain 'B' and (resid 44 through 123 )BB44 - 1231 - 67
99chain 'B' and (resid 124 through 274 )BB124 - 27468 - 218
1010chain 'B' and (resid 275 through 295 )BB275 - 295219 - 239

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