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- PDB-6ped: Crystal structure of HEMK2-TRMT112 complex -

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Basic information

Entry
Database: PDB / ID: 6ped
TitleCrystal structure of HEMK2-TRMT112 complex
Components
  • Methyltransferase N6AMT1
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsTRANSFERASE / methyltransferase / complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


arsonoacetate metabolic process / methylarsonite 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 / methylarsonite 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 / tRNA methylation / positive regulation of rRNA processing / S-adenosyl-L-methionine binding / rRNA modification in the nucleus and cytosol / rRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / 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 superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Multifunctional methyltransferase subunit TRM112-like protein / Methyltransferase N6AMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsDong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of HEMK2-TRMT112 complex
Authors: Dong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)41,81215
Polymers41,4272
Non-polymers38413
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.539, 110.539, 131.972
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 / Methylarsonite methyltransferase N6AMT1 / ...HemK methyltransferase family member 2 / M.HsaHemK2P / Methylarsonite methyltransferase N6AMT1 / N(6)-adenine-specific DNA methyltransferase 1 / Protein N(5)-glutamine methyltransferase


Mass: 25011.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, PRED28 / Plasmid: pET28a-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V3R
References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases, site-specific DNA-methyltransferase (adenine-specific)
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog


Mass: 16415.748 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 / Plasmid: pET15a-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V3R / References: UniProt: Q9UI30
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2 M sodium/potassium phosphate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.3→47.86 Å / Num. obs: 21722 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.017 / Rrim(I) all: 0.074 / Net I/σ(I): 27.4 / Num. measured all: 412065 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3819.31.3863941920450.7860.321.4232.199.9
8.92-47.8614.10.02865014610.9990.0080.02983.899.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: isomorphous PDB entry 6k0x

6k0x


Resolution: 2.3→47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.252 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. Authors are unsure about the identity of the ligand that is currently modeled as SAH. Weak difference ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. Authors are unsure about the identity of the ligand that is currently modeled as SAH. Weak difference density suggests that the binding site may be occupied aternately by SAH or SAM.
RfactorNum. reflection% reflection
Rfree0.2425 1151 5.3 %
Rwork0.1921 --
obs0.1948 20525 99.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.23 Å2 / Biso mean: 54.211 Å2 / Biso min: 32.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å2-0 Å2
2---0.52 Å20 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 2.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 38 0 2361
Biso mean--50.07 --
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132413
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172264
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.6383299
X-RAY DIFFRACTIONr_angle_other_deg1.3971.5575222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5375319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25722.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8061510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
LS refinement shellResolution: 2.302→2.362 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 67 -
Rwork0.263 1473 -
all-1540 -
obs--99.74 %

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