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- PDB-5nfj: Crystal structure of the methyltransferase subunit of human mitoc... -

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Basic information

Entry
Database: PDB / ID: 5nfj
TitleCrystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)
ComponentsMitochondrial ribonuclease P protein 1
KeywordsTRANSFERASE / SPOUT / methylation / tRNA / TRMT10C / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / mRNA (adenine-N1-)-methyltransferase activity / : / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / tRNA (guanine9-N1)-methyltransferase / mitochondrial ribonuclease P complex ...mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / mRNA (adenine-N1-)-methyltransferase activity / : / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / tRNA (guanine9-N1)-methyltransferase / mitochondrial ribonuclease P complex / tRNA (guanosine(9)-N1)-methyltransferase activity / mitochondrial tRNA 5'-end processing / mitochondrial tRNA 3'-end processing / : / tRNA modification in the mitochondrion / tRNA methyltransferase complex / : / positive regulation of mitochondrial translation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
tRNA methyltransferase 10 homologue C / tRNA (guanine-N1-)-methyltransferase, eukaryotic / tRNA methyltransferase TRM10-type domain / tRNA methyltransferase TRM10-type domain superfamily / SAM-dependent methyltransferase TRM10-type domain profile. / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / tRNA methyltransferase 10 homolog C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsOerum, S. / Kopec, J. / Fitzpatrick, F. / Newman, J.A. / Chalk, R. / Shrestha, L. / Fairhead, M. / Talon, R. / Burgess-Brown, N. / von Delft, F. ...Oerum, S. / Kopec, J. / Fitzpatrick, F. / Newman, J.A. / Chalk, R. / Shrestha, L. / Fairhead, M. / Talon, R. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, C. / Bountra, C. / Oppermann, U. / Yue, W.W. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)
Authors: Oerum, S. / Kopec, J. / Fitzpatrick, F. / Newman, J.A. / Oppermann, U. / Yue, W.W.
History
DepositionMar 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial ribonuclease P protein 1
B: Mitochondrial ribonuclease P protein 1
C: Mitochondrial ribonuclease P protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,49317
Polymers71,4053
Non-polymers2,08814
Water3,909217
1
A: Mitochondrial ribonuclease P protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6007
Polymers23,8021
Non-polymers7996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitochondrial ribonuclease P protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6007
Polymers23,8021
Non-polymers7996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitochondrial ribonuclease P protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2923
Polymers23,8021
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.640, 82.640, 148.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Mitochondrial ribonuclease P protein 1 / Mitochondrial RNase P protein 1 / HBV pre-S2 trans-regulated protein 2 / RNA (guanine-9-)- ...Mitochondrial RNase P protein 1 / HBV pre-S2 trans-regulated protein 2 / RNA (guanine-9-)-methyltransferase domain-containing protein 1 / Renal carcinoma antigen NY-REN-49 / tRNA methyltransferase 10 homolog C


Mass: 23801.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT10C, MRPP1, RG9MTD1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7L0Y3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.43 Å3/Da / Density % sol: 64.2 % / Description: Diamonds
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Well solution: 12% PEG 1000, 28% glycerol, 1.5%(w/v) PEG 3350 Cryo: 25% propylene glycol Protein concentration: 11 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.96→82.64 Å / Num. obs: 67692 / % possible obs: 99.98 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→82.64 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.148 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20648 3570 5 %RANDOM
Rwork0.18533 ---
obs0.18649 67692 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.966 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å2-0 Å2-0 Å2
2--1.37 Å2-0 Å2
3----2.74 Å2
Refinement stepCycle: 1 / Resolution: 1.96→82.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 139 217 4743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194641
X-RAY DIFFRACTIONr_bond_other_d0.0010.024346
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9896264
X-RAY DIFFRACTIONr_angle_other_deg1.074310111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29624.521219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89415852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5491527
X-RAY DIFFRACTIONr_chiral_restr0.1210.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214949
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02923
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6725.1932144
X-RAY DIFFRACTIONr_mcbond_other4.6715.1932144
X-RAY DIFFRACTIONr_mcangle_it6.4537.7532671
X-RAY DIFFRACTIONr_mcangle_other6.4527.7522672
X-RAY DIFFRACTIONr_scbond_it5.4955.7742497
X-RAY DIFFRACTIONr_scbond_other5.4955.7742497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9038.4333591
X-RAY DIFFRACTIONr_long_range_B_refined9.91459.8224989
X-RAY DIFFRACTIONr_long_range_B_other9.91659.7044958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 262 -
Rwork0.335 5015 -
obs--99.96 %

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