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- PDB-6aax: Crystal structure of TFB1M and h45 with SAM in homo sapiens -

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Basic information

Entry
Database: PDB / ID: 6aax
TitleCrystal structure of TFB1M and h45 with SAM in homo sapiens
Components
  • Dimethyladenosine transferase 1, mitochondrial
  • RNA (28-mer)
KeywordsTRANSFERASE/RNA / TFB1M / h45 / TRANSFERASE-RNA complex
Function / homology
Function and homology information


rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / mitochondrial matrix ...rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / mitochondrial matrix / DNA binding / RNA binding
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / Dimethyladenosine transferase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsLiu, X. / Shen, S. / Wu, P. / Li, F. / Gong, Q. / Wu, J. / Zhang, H. / Shi, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31330018 China
Chinese Academy of SciencesXDPB10, XDB08010101 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function.
Authors: Liu, X. / Shen, S. / Wu, P. / Li, F. / Liu, X. / Wang, C. / Gong, Q. / Wu, J. / Yao, X. / Zhang, H. / Shi, Y.
History
DepositionJul 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Dimethyladenosine transferase 1, mitochondrial
B: RNA (28-mer)
C: Dimethyladenosine transferase 1, mitochondrial
D: RNA (28-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2187
Polymers91,3154
Non-polymers9033
Water0
1
A: Dimethyladenosine transferase 1, mitochondrial
B: RNA (28-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1624
Polymers45,6582
Non-polymers5052
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-6 kcal/mol
Surface area16940 Å2
MethodPISA
2
C: Dimethyladenosine transferase 1, mitochondrial
D: RNA (28-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0563
Polymers45,6582
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-8 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.120, 104.120, 449.378
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 Dimethyladenosine transferase 1, mitochondrial / Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / mtTFB1 / S- ...Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / mtTFB1 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 1


Mass: 36622.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFB1M, CGI-75 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WVM0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (28-mer) / helix 45


Mass: 9035.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3

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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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M potassium chloride, 0.025M magnesium sulfate hydrate, 0.05M HEPES sodium, pH 7.0, 20% v/v polyethylene glycol 200

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 30398 / % possible obs: 100 % / Redundancy: 42 % / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.042 / Rrim(I) all: 0.225 / Χ2: 1.373 / Net I/σ(I): 4.1 / Num. measured all: 1275274
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2Rmerge(I) obsRrim(I) all
3-3.114329470.8140.3531.096
3.11-3.2343.329480.9210.2161.124
3.23-3.3843.229520.9630.1481.1740.9680.98
3.38-3.5643.129610.980.1091.2380.7170.725
3.56-3.7842.830020.990.0741.2860.4840.49
3.78-4.0742.729890.9960.0481.3280.3140.317
4.07-4.4842.430310.9970.0351.3930.2310.234
4.48-5.1341.730560.9980.0281.6350.180.182
5.13-6.4640.431390.9980.0281.7480.1770.18
6.46-4037.6337310.011.7130.0630.064

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GC5

4gc5


Resolution: 2.994→38.627 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 1473 4.87 %
Rwork0.2222 28795 -
obs0.2245 30268 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.21 Å2 / Biso mean: 71.0973 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.994→38.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 1202 61 0 5735
Biso mean--81.63 --
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095980
X-RAY DIFFRACTIONf_angle_d1.2088408
X-RAY DIFFRACTIONf_chiral_restr0.0571010
X-RAY DIFFRACTIONf_plane_restr0.007873
X-RAY DIFFRACTIONf_dihedral_angle_d10.1683467
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9938-3.09040.37961510.32552500265199
3.0904-3.20080.34671170.273625562673100
3.2008-3.32890.31051270.27225652692100
3.3289-3.48030.34171350.252425812716100
3.4803-3.66360.31691520.248325262678100
3.6636-3.8930.28581240.231125822706100
3.893-4.19320.28111210.206326272748100
4.1932-4.61460.21961360.182426112747100
4.6146-5.28090.19031390.186226522791100
5.2809-6.64780.27231150.226227132828100
6.6478-38.62990.25121560.2072882303899
Refinement TLS params.Method: refined / Origin x: 0.6772 Å / Origin y: 31.392 Å / Origin z: -23.2634 Å
111213212223313233
T0.4985 Å20.1105 Å20.1448 Å2-0.654 Å20.4231 Å2--0.6787 Å2
L0.0788 °2-0.0481 °20.1496 °2-0.4738 °2-0.2713 °2--0.5593 °2
S0.0602 Å °-0.1086 Å °-0.0845 Å °0.1608 Å °-0.0112 Å °-0.0519 Å °0.0971 Å °-0.0126 Å °0.149 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allE2 - 1
2X-RAY DIFFRACTION1allG1
3X-RAY DIFFRACTION1allA35 - 324
4X-RAY DIFFRACTION1allB922 - 949
5X-RAY DIFFRACTION1allC34 - 325
6X-RAY DIFFRACTION1allD922 - 949

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