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- PDB-6kms: Crystal structure of human N6amt1-Trm112 in complex with SAM (spa... -

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Basic information

Entry
Database: PDB / ID: 6kms
TitleCrystal structure of human N6amt1-Trm112 in complex with SAM (space group I422)
Components
  • Methyltransferase N6AMT1
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsTRANSFERASE / methyltransferase / complex / protein translation / polypeptide release factor eRF1
Function / homology
Function and homology information


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 ...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 / histone H4K12 methyltransferase activity / 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
S-ADENOSYLMETHIONINE / Multifunctional methyltransferase subunit TRM112-like protein / Methyltransferase N6AMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsLi, W.J. / Shi, Y. / Zhang, T.L. / Ye, J. / Ding, J.P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31530013 China
National Natural Science Foundation of China31800622 China
CitationJournal: Cell Discov / Year: 2019
Title: Structural insight into human N6amt1-Trm112 complex functioning as a protein methyltransferase.
Authors: Li, W. / Shi, Y. / Zhang, T. / Ye, J. / Ding, J.
History
DepositionAug 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,8106
Polymers79,0134
Non-polymers7972
Water00
1
C: Methyltransferase N6AMT1
A: Multifunctional methyltransferase subunit TRM112-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9053
Polymers39,5062
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area13900 Å2
MethodPISA
2
B: Multifunctional methyltransferase subunit TRM112-like protein
D: Methyltransferase N6AMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9053
Polymers39,5062
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-17 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.354, 195.354, 246.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 43 or (resid 44...
21(chain B and resid 0 through 120)
12(chain C and (resid 6 through 15 or (resid 16...
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111MSEMSEALAALA(chain A and (resid 0 through 43 or (resid 44...AB0 - 431 - 44
121ARGARGARGARG(chain A and (resid 0 through 43 or (resid 44...AB4445
131MSEMSEGLUGLU(chain A and (resid 0 through 43 or (resid 44...AB0 - 1201 - 121
211MSEMSEGLUGLU(chain B and resid 0 through 120)BC0 - 1201 - 121
112PHEPHEGLYGLY(chain C and (resid 6 through 15 or (resid 16...CA6 - 1520 - 29
122ARGARGARGARG(chain C and (resid 6 through 15 or (resid 16...CA1630
132ASNASNSERSER(chain C and (resid 6 through 15 or (resid 16...CA5 - 21419 - 228
142ASNASNSERSER(chain C and (resid 6 through 15 or (resid 16...CA5 - 21419 - 228
152ASNASNSERSER(chain C and (resid 6 through 15 or (resid 16...CA5 - 21419 - 228
212PHEPHESERSERchain DDD6 - 21420 - 228

NCS ensembles :
ID
1
2

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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: 24878.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, PRED28 / Production host: Escherichia coli K-12 (bacteria)
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: 14627.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9UI30
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 7.95 Å3/Da / Density % sol: 83.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M (NH4)2SO4, 0.1M MES, pH 6.5, 10% 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 39672 / % possible obs: 100 % / Redundancy: 28.8 % / Biso Wilson estimate: 83.4 Å2 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.044 / Rrim(I) all: 0.239 / Χ2: 1.951 / Net I/σ(I): 26.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.3128.12.20339000.7680.422.2441.282100
3.31-3.4528.31.45838990.8690.2771.4851.297100
3.45-3.628.60.88439010.9440.1670.91.356100
3.6-3.79290.59739540.9770.1120.6081.404100
3.79-4.0329.30.41639290.9860.0780.4231.476100
4.03-4.3429.50.27839350.9930.0520.2831.685100
4.34-4.7829.30.19739760.9960.0370.22.108100
4.78-5.47290.16939710.9970.0320.1722.245100
5.47-6.8928.20.13940270.9980.0260.1422.314100
6.89-5028.30.07341800.9990.0140.0744.20599.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→39.386 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 1978 5.01 %
Rwork0.2315 37504 -
obs0.2333 39482 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.41 Å2 / Biso mean: 81.6587 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→39.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 54 0 5097
Biso mean--73.92 --
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125209
X-RAY DIFFRACTIONf_angle_d1.3747094
X-RAY DIFFRACTIONf_chiral_restr0.072827
X-RAY DIFFRACTIONf_plane_restr0.009922
X-RAY DIFFRACTIONf_dihedral_angle_d21.8713114
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A953X-RAY DIFFRACTION21.7TORSIONAL
12B953X-RAY DIFFRACTION21.7TORSIONAL
21C1670X-RAY DIFFRACTION21.7TORSIONAL
22D1670X-RAY DIFFRACTION21.7TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2-3.280.35881190.36112652
3.28-3.36870.38541420.34772647
3.3687-3.46770.36211560.30722622
3.4677-3.57960.34161630.29542614
3.5796-3.70740.34511330.28362642
3.7074-3.85580.26021460.26692660
3.8558-4.03110.29021450.26462640
4.0311-4.24340.32051280.2432683
4.2434-4.50890.22291430.2172648
4.5089-4.85640.2261510.20762673
4.8564-5.34410.25091300.2122704
5.3441-6.11490.29481380.22452713
6.1149-7.69470.2491410.21232742
7.6947-39.3860.20191430.16532864

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