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- PDB-8qdg: compound 1a bound KMT9 crystal structure -

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Basic information

Entry
Database: PDB / ID: 8qdg
Titlecompound 1a 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 / cytosol / cytoplasm
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: 1.392 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)36,5133
Polymers36,0762
Non-polymers4361
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-14 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.852, 109.852, 130.709
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-SDU / (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})-pyrrolidin-3-yl]amino]-2-azanyl-butanoic acid


Mass: 436.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28N8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.2 M Na3Citrate, 0.1M Tris 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.39→47.613 Å / Num. obs: 93172 / % possible obs: 99.9 % / Redundancy: 39 % / CC1/2: 1 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.035 / Rrim(I) all: 0.157 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
7.62-47.5732.80.03370210.0070.03399.6
1.39-1.4236.74.92144540.4121.1515.05598.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
REFMAC5.8.0352refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.392→47.613 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.141 / SU B: 1.952 / SU ML: 0.033 / Average fsc free: 0.9723 / Average fsc work: 0.9803 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 4709 5.058 %
Rwork0.1521 88387 -
all0.153 --
obs-93096 99.935 %
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: 22.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.024 Å20.012 Å20 Å2
2--0.024 Å2-0 Å2
3----0.079 Å2
Refinement stepCycle: LAST / Resolution: 1.392→47.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 31 167 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122602
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162457
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.6483556
X-RAY DIFFRACTIONr_angle_other_deg0.6091.5515760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.235519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81410454
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.19210111
X-RAY DIFFRACTIONr_chiral_restr0.0910.2412
X-RAY DIFFRACTIONr_chiral_restr_other0.0170.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
X-RAY DIFFRACTIONr_nbd_refined0.2350.2422
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22208
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21225
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2105
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.236
X-RAY DIFFRACTIONr_nbd_other0.2330.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.217
X-RAY DIFFRACTIONr_mcbond_it4.8292.0161287
X-RAY DIFFRACTIONr_mcbond_other4.8952.0151287
X-RAY DIFFRACTIONr_mcangle_it5.3763.0241614
X-RAY DIFFRACTIONr_mcangle_other5.3743.0281615
X-RAY DIFFRACTIONr_scbond_it9.6242.5921315
X-RAY DIFFRACTIONr_scbond_other9.6212.5941316
X-RAY DIFFRACTIONr_scangle_it8.7433.6391928
X-RAY DIFFRACTIONr_scangle_other8.743.6411929
X-RAY DIFFRACTIONr_lrange_it8.25429.7642719
X-RAY DIFFRACTIONr_lrange_other8.25229.5552693
X-RAY DIFFRACTIONr_rigid_bond_restr13.81135059
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
1.392-1.4280.313380.2863780.28167530.930.94299.45210.28
1.428-1.4670.2693320.24262820.24466140.9490.9591000.24
1.467-1.5090.2383210.21661250.21764460.9610.9681000.208
1.509-1.5560.2143620.18958860.1962480.9690.9771000.174
1.556-1.6070.2183180.16557380.16860560.9670.9821000.146
1.607-1.6630.22830.14856220.15159050.9730.9861000.128
1.663-1.7260.1743020.13653700.13856720.9810.9881000.113
1.726-1.7960.1822650.12952200.13254850.9780.9891000.108
1.796-1.8760.1682560.1250160.12252720.9830.9911000.099
1.876-1.9670.1652620.11647790.11850410.9830.9921000.097
1.967-2.0730.162360.12245620.12347980.9860.9911000.104
2.073-2.1990.1672140.13343510.13445650.9830.991000.116
2.199-2.350.1662100.13940620.1442720.9840.9881000.122
2.35-2.5380.172140.14238100.14340240.9820.9881000.124
2.538-2.7790.1712000.14335200.14437200.9840.9871000.127
2.779-3.1060.1861920.16231890.16333810.9780.9831000.147
3.106-3.5840.1551380.1528650.1530030.9850.9861000.144
3.584-4.3840.1421180.13524680.13525860.9880.9891000.136
4.384-6.1730.19930.16219550.16420480.9850.9881000.166
6.173-47.6130.213550.21411900.21412450.9760.9751000.221
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)
10.03510.0031-0.05680.0854-0.03740.1049-0.0022-0.00920.00150.00280.0018-0.00380.00180.01410.00040.00270.0003-0.00130.0026-0.00040.0024-42.1268-6.7632-16.3652
20.06690.0101-0.03460.0090.02070.11820.00060.00380.0007-0.0008-0.00110.0007-0.0027-0.01210.00060.00220.0002-0.00040.00220.00040.0003-47.0389-26.7729-2.4698
Refinement TLS groupSelection: ALL

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