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- PDB-4n49: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein ... -

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Basic information

Entry
Database: PDB / ID: 4n49
TitleCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein in complex with m7GpppG and SAM
ComponentsCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
KeywordsTRANSFERASE / methyltransferase / mRNA cap methylation / mRNA
Function / homology
Function and homology information


: / : / 7-methylguanosine mRNA capping / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / nucleic acid binding / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Rossmann fold - #12760 / RrmJ-type ribose 2-O-methyltransferase domain / RrmJ-type ribose 2'-O-methyltransferase (EC 2.1.1.57) domain profile. / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / WW/rsp5/WWP domain signature. / Domain with 2 conserved Trp (W) residues / WW domain ...Rossmann fold - #12760 / RrmJ-type ribose 2-O-methyltransferase domain / RrmJ-type ribose 2'-O-methyltransferase (EC 2.1.1.57) domain profile. / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / WW/rsp5/WWP domain signature. / Domain with 2 conserved Trp (W) residues / WW domain / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYLMETHIONINE / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSmietanski, M. / Werener, M. / Purta, E. / Kaminska, K.H. / Stepinski, J. / Darzynkiewicz, E. / Nowotny, M. / Bujnicki, J.M.
CitationJournal: Nat Commun / Year: 2014
Title: Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation.
Authors: Smietanski, M. / Werner, M. / Purta, E. / Kaminska, K.H. / Stepinski, J. / Darzynkiewicz, E. / Nowotny, M. / Bujnicki, J.M.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8964
Polymers48,9361
Non-polymers9613
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.834, 87.619, 57.310
Angle α, β, γ (deg.)90.00, 112.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 / Cap1 2'O-ribose methyltransferase 1 / MTr1 / hMTr1 / FtsJ methyltransferase domain-containing ...Cap1 2'O-ribose methyltransferase 1 / MTr1 / hMTr1 / FtsJ methyltransferase domain-containing protein 2 / Interferon-stimulated gene 95 kDa protein / ISG95


Mass: 48935.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTSJD2, KIAA0082, MTR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N1G2, methyltransferase cap1
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 30% PEG 3350, 100 mM Bis-Tris [pH 6.5], and 100 mM NaBr, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2011
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→46.8 Å / Num. all: 36471 / Num. obs: 36369 / % possible obs: 99.7 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N4A

4n4a


Resolution: 1.9→46.8 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1818 5 %random
Rwork0.1538 ---
obs0.1563 36369 99.72 %-
all-36471 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 60 542 3823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123428
X-RAY DIFFRACTIONf_angle_d1.3024662
X-RAY DIFFRACTIONf_dihedral_angle_d14.5421279
X-RAY DIFFRACTIONf_chiral_restr0.089500
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.95140.3051380.26342610X-RAY DIFFRACTION99
1.9514-2.00890.26221390.21582645X-RAY DIFFRACTION100
2.0089-2.07370.28351400.19552657X-RAY DIFFRACTION100
2.0737-2.14780.23451390.17762642X-RAY DIFFRACTION100
2.1478-2.23380.20821400.17122649X-RAY DIFFRACTION100
2.2338-2.33550.21141380.16772632X-RAY DIFFRACTION99
2.3355-2.45860.2051400.15082662X-RAY DIFFRACTION100
2.4586-2.61260.23231410.14852664X-RAY DIFFRACTION100
2.6126-2.81430.19111400.1542671X-RAY DIFFRACTION100
2.8143-3.09750.20761390.15232641X-RAY DIFFRACTION100
3.0975-3.54560.1891410.13992678X-RAY DIFFRACTION100
3.5456-4.46650.1611420.11862687X-RAY DIFFRACTION100
4.4665-46.84380.16441410.13032713X-RAY DIFFRACTION100

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