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- PDB-4n48: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein ... -

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Basic information

Entry
Database: PDB / ID: 4n48
TitleCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 Protein in complex with capped RNA fragment
Components
  • Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
  • capped RNA
KeywordsTRANSFERASE/RNA / methyltransferase / mRNA cap methylation / capped mRNA / TRANSFERASE-RNA complex
Function / homology
Function and homology information


7-methylguanosine mRNA capping / mRNA processing / methyltransferase cap1 / methylation / methyltransferase cap1 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 ...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 / RNA / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
B: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
D: capped RNA
G: capped RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2288
Polymers100,3534
Non-polymers1,8754
Water2,342130
1
B: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
G: capped RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1144
Polymers50,1772
Non-polymers9382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1
D: capped RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1144
Polymers50,1772
Non-polymers9382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.209, 60.038, 87.045
Angle α, β, γ (deg.)90.23, 97.83, 116.25
Int Tables number1
Space group name H-MP1

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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.: 2
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: RNA chain capped RNA


Mass: 1240.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic RNA
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
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: RAYONIX MX-225 / Detector: CCD / Date: Mar 13, 2012
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: 2.7→30.334 Å / Num. all: 26308 / Num. obs: 24703 / % possible obs: 93.9 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9
Reflection shellResolution: 2.7→2.86 Å / % possible all: 94.5

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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 4N49

4n49


Resolution: 2.704→30.334 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 1248 5.05 %
Rwork0.182 --
obs0.185 24703 96.56 %
all-25583 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.704→30.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 148 118 130 6807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046847
X-RAY DIFFRACTIONf_angle_d0.7919298
X-RAY DIFFRACTIONf_dihedral_angle_d13.9952525
X-RAY DIFFRACTIONf_chiral_restr0.0551013
X-RAY DIFFRACTIONf_plane_restr0.0031167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.704-2.81230.26181360.20732487X-RAY DIFFRACTION93
2.8123-2.94020.32031380.22682622X-RAY DIFFRACTION97
2.9402-3.09510.29941380.22012643X-RAY DIFFRACTION98
3.0951-3.28880.27461420.20582659X-RAY DIFFRACTION98
3.2888-3.54230.23711380.19222608X-RAY DIFFRACTION97
3.5423-3.89820.2121370.16572595X-RAY DIFFRACTION97
3.8982-4.46070.23261410.16072647X-RAY DIFFRACTION97
4.4607-5.61420.21481390.16322609X-RAY DIFFRACTION96
5.6142-30.33570.21261390.16662585X-RAY DIFFRACTION96

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