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- PDB-6k0x: Structure of N6AMT1-TRMT112 Complex with SAM -

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Basic information

Entry
Database: PDB / ID: 6k0x
TitleStructure of N6AMT1-TRMT112 Complex with SAM
Components
  • Methyltransferase N6AMT1
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsGENE REGULATION / Methylase / Complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


methylarsonite methyltransferase activity / arsonoacetate metabolic process / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / rRNA (guanine-N7)-methylation / peptidyl-glutamine methylation / DNA methylation on adenine / toxin metabolic process / tRNA modification in the nucleus and cytosol / positive regulation of rRNA processing ...methylarsonite methyltransferase activity / arsonoacetate metabolic process / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / rRNA (guanine-N7)-methylation / peptidyl-glutamine methylation / DNA methylation on adenine / toxin metabolic process / tRNA modification in the nucleus and cytosol / positive regulation of rRNA processing / site-specific DNA-methyltransferase (adenine-specific) activity / histone lysine methylation / Methylation / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / protein methyltransferase activity / S-adenosyl-L-methionine binding / rRNA modification in the nucleus and cytosol / rRNA methylation / histone-lysine N-methyltransferase activity / Eukaryotic Translation Termination / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / positive regulation of cell growth / 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
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Multifunctional methyltransferase subunit TRM112-like protein / Methyltransferase N6AMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGuo, Q. / Liao, S. / Xu, C. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Structure of HEMK2-TRM112 Complex with SAM
Authors: Guo, Q. / Liao, S. / Xu, C.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: 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)37,6623
Polymers37,2642
Non-polymers3981
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)109.607, 109.607, 130.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-247-

HOH

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Components

#1: Protein Methyltransferase N6AMT1


Mass: 23048.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases, site-specific DNA-methyltransferase (adenine-specific)
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein


Mass: 14215.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9UI30
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium acetate 0.1M sodium citrate tribasic dihydrate PH 5.6 30% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24031 / % possible obs: 99.8 % / Redundancy: 36.3 % / Net I/σ(I): 28
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 2346

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q87,4QTU
Resolution: 2.2→34.05 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2135 1264 5.26 %
Rwork0.1744 --
obs0.1764 24031 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 27 117 2549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072511
X-RAY DIFFRACTIONf_angle_d0.9173426
X-RAY DIFFRACTIONf_dihedral_angle_d17.6591538
X-RAY DIFFRACTIONf_chiral_restr0.055404
X-RAY DIFFRACTIONf_plane_restr0.006444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.28810.24281250.19882481X-RAY DIFFRACTION99
2.2881-2.39220.31251410.19452462X-RAY DIFFRACTION100
2.3922-2.51830.24531370.19852484X-RAY DIFFRACTION100
2.5183-2.6760.26641270.20542509X-RAY DIFFRACTION100
2.676-2.88260.23471420.20062504X-RAY DIFFRACTION100
2.8826-3.17250.23981470.19062496X-RAY DIFFRACTION100
3.1725-3.63110.1731400.1572549X-RAY DIFFRACTION100
3.6311-4.5730.17331460.13482577X-RAY DIFFRACTION100
4.573-34.05440.20631590.182705X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.39060.57820.81127.85770.5263.21950.0252-0.2991-0.3313-0.03890.0349-0.18160.33090.2697-0.030.2460.08940.0280.37620.03430.236622.814236.572875.3374
23.9659-0.8943-0.752.53320.67962.6027-0.0621-0.04430.05430.11140.0431-0.090.05690.12430.02140.1590.03810.00020.19110.01430.193112.403244.518878.4415
36.8691-0.1777-2.44832.66140.37823.1492-0.535-0.0331-1.19780.25370.35990.44481.0023-0.6690.19170.73130.05630.06450.8141-0.07940.65189.58527.364865.9344
43.8842-1.2668-0.8422.9181-0.04973.16090.10920.43320.0396-0.3021-0.1826-0.19030.1091-0.04790.08040.24660.05560.04990.29520.02890.224418.315940.893661.9016
53.07060.3387-0.02515.07841.03743.65620.03260.4034-0.0001-0.6171-0.02770.232-0.3121-0.1544-0.01110.18630.02390.00510.16530.00090.184-3.734350.721175.4032
62.7835-0.18220.28495.7984-2.26979.79650.1176-0.371-0.44460.3540.07010.3276-0.0002-0.6898-0.13890.1936-0.04670.02330.16880.010.2102-4.215646.984991.614
75.6648-1.56373.81953.9312-0.91328.3611-0.15560.1601-0.1202-0.11440.1328-0.4686-0.70111.091-0.02740.2978-0.12580.00430.35130.02060.295612.207759.202485.9202
88.01861.3771-4.73482.7399-5.02699.91410.1843-0.04270.65890.29950.09040.7654-0.5181-0.7312-0.32680.3080.0344-0.01790.2648-0.04520.3579-4.209159.342584.1651
93.6173-1.19611.391441.14943.1001-0.01660.07030.44960.2840.33230.7532-0.6420.2842-0.29610.5665-0.05230.00650.2156-0.05170.2774-1.482264.564789.833
106.28841.95720.92885.76010.26533.66960.1038-0.33640.14550.9279-0.3043-0.8515-0.87440.7330.13040.4662-0.1086-0.07250.26150.01330.22778.334664.068390.159
115.890.7124.07073.8391.39187.08360.17340.0492-0.2182-0.0372-0.070.0812-0.0317-0.245-0.15290.13530.00980.03740.19520.0170.2139-6.480645.697882.4477
124.4081.52054.22385.58021.63214.40310.4070.571-0.9332-0.51180.09080.26490.99090.1032-0.3720.28440.0256-0.02640.3261-0.07650.2785-3.454238.637176.3248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 214 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 23 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 60 )
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 73 )
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 89 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 123 )

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