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- PDB-9fim: compound 1 bound KMT9 crystal structure -

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Basic information

Entry
Database: PDB / ID: 9fim
Titlecompound 1 bound KMT9 crystal structure
Components
  • Methyltransferase N6AMT1
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsTRANSFERASE / Protein transferase / gene regulation
Function / homology
Function and homology information


histone H4K12 methyltransferase activity / arsonoacetate metabolic process / arsenite methyltransferase activity / protein-glutamine N-methyltransferase activity / eRF1 methyltransferase complex / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process ...histone H4K12 methyltransferase activity / arsonoacetate metabolic process / arsenite methyltransferase activity / protein-glutamine N-methyltransferase activity / eRF1 methyltransferase complex / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / 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 / tRNA methylation / positive regulation of rRNA processing / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / rRNA methylation / rRNA modification in the nucleus and cytosol / negative regulation of gene expression, epigenetic / Eukaryotic Translation Termination / maturation of LSU-rRNA / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of SSU-rRNA / positive regulation of cell growth / methylation / nucleic acid binding / protein heterodimerization activity / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytoplasm / 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 HEMK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSheng, W. / Eric, M. / Roland, S.
Funding support Germany, 4items
OrganizationGrant numberCountry
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
DepositionMay 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)36,5453
Polymers36,0762
Non-polymers4681
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-13 kcal/mol
Surface area14050 Å2
Unit cell
Length a, b, c (Å)110.027, 110.027, 129.737
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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-A1IC3 / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]amino]-2-azanyl-butanoic acid


Mass: 468.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28N8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.1 M Na3Citrate, 0.1M Tris 8.5

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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 / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.64 Å / Num. obs: 61536 / % possible obs: 100 % / Redundancy: 39 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29.8
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 2993 / CC1/2: 0.765 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.64 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.462 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1866 3057 4.973 %
Rwork0.159 58411 -
all0.16 --
obs-61468 99.99 %
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: 29.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.225 Å2-0.113 Å2-0 Å2
2---0.225 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 33 116 2584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162474
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.8483467
X-RAY DIFFRACTIONr_angle_other_deg0.6121.735722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.065516
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.128101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35210433
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.77510104
X-RAY DIFFRACTIONr_chiral_restr0.0920.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.2310.2452
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22273
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21255
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.217
X-RAY DIFFRACTIONr_nbd_other0.2090.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.222
X-RAY DIFFRACTIONr_mcbond_it5.3032.0721275
X-RAY DIFFRACTIONr_mcbond_other5.2722.0711275
X-RAY DIFFRACTIONr_mcangle_it7.9473.7261594
X-RAY DIFFRACTIONr_mcangle_other7.9593.731595
X-RAY DIFFRACTIONr_scbond_it7.3582.4281269
X-RAY DIFFRACTIONr_scbond_other7.3562.431270
X-RAY DIFFRACTIONr_scangle_it10.7334.3021869
X-RAY DIFFRACTIONr_scangle_other10.7314.3041870
X-RAY DIFFRACTIONr_lrange_it14.34521.0072688
X-RAY DIFFRACTIONr_lrange_other14.30120.812670
X-RAY DIFFRACTIONr_rigid_bond_restr3.83535018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2722140.2374257X-RAY DIFFRACTION100
1.642-1.6860.232450.2064112X-RAY DIFFRACTION100
1.686-1.7350.2122370.1793998X-RAY DIFFRACTION100
1.735-1.7890.2012050.153915X-RAY DIFFRACTION100
1.789-1.8470.1681970.1233801X-RAY DIFFRACTION99.975
1.847-1.9120.1681760.1223686X-RAY DIFFRACTION100
1.912-1.9840.1692040.1323540X-RAY DIFFRACTION100
1.984-2.0650.1571790.1323428X-RAY DIFFRACTION100
2.065-2.1560.161550.143327X-RAY DIFFRACTION100
2.156-2.2610.1661580.1363155X-RAY DIFFRACTION100
2.261-2.3840.1511510.1363021X-RAY DIFFRACTION100
2.384-2.5280.2021430.1542859X-RAY DIFFRACTION100
2.528-2.7020.1991370.1632702X-RAY DIFFRACTION100
2.702-2.9170.2251400.1822509X-RAY DIFFRACTION100
2.917-3.1950.221180.1832341X-RAY DIFFRACTION100
3.195-3.570.1811140.1672124X-RAY DIFFRACTION100
3.57-4.1180.14760.1461916X-RAY DIFFRACTION100
4.118-5.0340.156820.1361642X-RAY DIFFRACTION100
5.034-7.080.207940.1941271X-RAY DIFFRACTION100
7.08-47.640.303320.203807X-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)
10.70930.04420.06782.1652-0.50781.9494-0.02620.08420.0903-0.1301-0.0045-0.0232-0.08920.10130.03080.0549-0.002-0.01930.01570.00840.0222-42.1576-6.9337-16.5781
22.53670.1872-0.36461.6160.07852.13070.0117-0.0041-0.0016-0.026-0.06490.05220.052-0.10460.05330.03470.0012-0.01240.0078-0.00560.0079-46.1664-26.6883-3.0824
Refinement TLS groupSelection: ALL

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