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- PDB-8qdi: compound 1b bound KMT9 crystal structure -

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Basic information

Entry
Database: PDB / ID: 8qdi
Titlecompound 1b bound KMT9 crystal structure
Components
  • Methyltransferase N6AMT1
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsTRANSFERASE / Protein transferase / gene regulation
Function / homology
Function and homology information


arsonoacetate metabolic process / arsenite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity ...arsonoacetate metabolic process / arsenite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / positive regulation of rRNA processing / tRNA methylation / S-adenosyl-L-methionine binding / S-adenosylmethionine-dependent methyltransferase activity / rRNA methylation / rRNA modification in the nucleus and cytosol / negative regulation of gene expression, epigenetic / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of cell growth / methylation / nucleic acid binding / protein heterodimerization activity / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Eukaryotic/archaeal PrmC-related / : / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Multifunctional methyltransferase subunit TRM112-like protein / Methyltransferase N6AMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.467 Å
AuthorsSheng, W. / Eric, M. / Roland, S.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1381 Germany
German Research Foundation (DFG)SFB992 Germany
German Research Foundation (DFG)Schu688 Germany
German Research Foundation (DFG)EXC-2189 Germany
German Research Foundation (DFG)DKTK FR01-374 Germany
CitationJournal: To Be Published
Title: compound 1a bound KMT9 crystal structure
Authors: Sheng, W. / Eric, M. / Roland, S.
History
DepositionAug 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase N6AMT1
B: Multifunctional methyltransferase subunit TRM112-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5413
Polymers36,0762
Non-polymers4651
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-12 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.516, 110.516, 129.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-277-

HOH

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Components

#1: Protein Methyltransferase N6AMT1 / HemK methyltransferase family member 2 / M.HsaHemK2P / Lysine N-methyltransferase 9 / ...HemK methyltransferase family member 2 / M.HsaHemK2P / Lysine N-methyltransferase 9 / Methylarsonite methyltransferase N6AMT1 / Protein N(5)-glutamine methyltransferase


Mass: 21804.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, KMT9, PRED28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog


Mass: 14272.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30
#3: Chemical ChemComp-QII / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[(2~{R})-pyrrolidin-2-yl]ethyl]amino]-2-azanyl-butanoic acid


Mass: 464.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.1 M Na3Citrate, 0.1M HEPES 7.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.467→47.901 Å / Num. obs: 80097 / % possible obs: 99.8 % / Redundancy: 39.4 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.021 / Rrim(I) all: 0.097 / Net I/σ(I): 26.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.03-47.8534.30.03160610.0070.031
1.47-1.4929.64.18937930.4481.0864.331

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.467→47.901 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.045 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1905 4033 5.039 %
Rwork0.1576 75996 -
all0.159 --
obs-80029 99.782 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.636 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å2-0 Å2
2---0.3 Å20 Å2
3---0.975 Å2
Refinement stepCycle: LAST / Resolution: 1.467→47.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 33 184 2624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122570
X-RAY DIFFRACTIONr_bond_other_d0.0080.0162438
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.6463510
X-RAY DIFFRACTIONr_angle_other_deg0.6061.5515711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.481517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38110444
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.15410105
X-RAY DIFFRACTIONr_chiral_restr0.0920.2410
X-RAY DIFFRACTIONr_chiral_restr_other0.0440.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_nbd_refined0.2330.2406
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22194
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21235
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.219
X-RAY DIFFRACTIONr_nbd_other0.1770.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.224
X-RAY DIFFRACTIONr_mcbond_it6.1232.2361283
X-RAY DIFFRACTIONr_mcbond_other6.1142.2351283
X-RAY DIFFRACTIONr_mcangle_it6.6493.3461610
X-RAY DIFFRACTIONr_mcangle_other6.6523.3481611
X-RAY DIFFRACTIONr_scbond_it10.3852.8261287
X-RAY DIFFRACTIONr_scbond_other10.3812.8261288
X-RAY DIFFRACTIONr_scangle_it10.2843.9861891
X-RAY DIFFRACTIONr_scangle_other10.2813.9871892
X-RAY DIFFRACTIONr_lrange_it8.83831.2122698
X-RAY DIFFRACTIONr_lrange_other8.84330.3292668
X-RAY DIFFRACTIONr_rigid_bond_restr13.96235008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.467-1.5050.3832720.35554090.35658240.9490.94797.54460.352
1.505-1.5460.3743170.31353850.31657020.950.9691000.305
1.546-1.5910.2862710.25252570.25355280.9670.9791000.24
1.591-1.640.2373070.20250930.20454000.9750.9851000.187
1.64-1.6930.22300.16949790.17152090.9790.9871000.151
1.693-1.7530.1852400.13948300.14150700.9820.9891000.12
1.753-1.8190.1682340.12146360.12348700.9820.9911000.104
1.819-1.8930.1762420.12144720.12447160.9840.99299.95760.107
1.893-1.9770.1882270.13343190.13645460.980.9911000.121
1.977-2.0730.1642300.13940860.1443160.9860.9921000.129
2.073-2.1850.1771980.14539410.14641390.9850.9911000.136
2.185-2.3180.1651880.13937360.14139240.9830.9911000.13
2.318-2.4770.1762010.13734990.13937000.9810.991000.127
2.477-2.6750.1671820.14232590.14334440.9830.98899.91290.132
2.675-2.9290.1871700.15330410.15532110.980.9861000.143
2.929-3.2740.2041430.16927660.1729090.9710.9821000.162
3.274-3.7770.1441290.14324640.14325930.9860.9881000.143
3.777-4.6190.171130.13121230.13322360.9830.991000.137
4.619-6.5020.227850.18916800.19117670.9790.98599.88680.199
6.502-47.9010.26540.21310210.21510750.9640.9761000.228
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)
10.0149-0.01570.00050.05180.03370.03340.0014-0.0014-0.0031-0.0016-0.00150.00340.0005-0.00260.00010.0108-0.00110.00080.0110.00010.0012-42.4116-6.9182-16.5154
20.02020.0027-0.00980.0080.01140.02620.0010.0010.00110-0.00070.0003-0.0013-0.002-0.00030.01050.0003-0.00020.010.00020.0001-47.3507-26.8381-2.4533
Refinement TLS groupSelection: ALL

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