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- PDB-1ri3: Structure and mechanism of mRNA cap (guanine N-7) methyltransferase -

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Basic information

Entry
Database: PDB / ID: 1ri3
TitleStructure and mechanism of mRNA cap (guanine N-7) methyltransferase
ComponentsmRNA CAPPING ENZYME
KeywordsTRANSFERASE / methyltransferase / rna / cap / m7G / messenger rna cap
Function / homology
Function and homology information


mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA binding / nucleus
Similarity search - Function
mRNA cap guanine-N7 methyltransferase, eukaryotes / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MIR / Resolution: 2.5 Å
AuthorsFabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure and mechanism of mRNA cap (Guanine-n7) methyltransferase
Authors: Fabrega, C. / Hausmann, S. / Shen, V. / Shuman, S. / Lima, C.D.
History
DepositionNov 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: mRNA CAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2082
Polymers34,8241
Non-polymers3841
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.341, 63.341, 111.937
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein mRNA CAPPING ENZYME / mRNA cap (guanine N-7) methyltransferase Ecm1


Mass: 34823.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: ECU10_0380 / Plasmid: PSUMO-SMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q8SR66
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.86 Å3/Da / Density % sol: 33.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 1.2M Na/K tartrate, 50mM BIS/TRIS, 20mM DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16.5 mg/mlprotein1drop
2220 mM1dropNaCl
320 mMTris-HCl1droppH8.0
41 mMbeta-mercaptoethanol1drop
51.2 Msodium/pootassium tartrate1reservoir
650 mMbis-tris1reservoirpH6.0
720 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 12167 / Num. obs: 11425 / % possible obs: 93.9 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.4 Å / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 189434
Reflection shell
*PLUS
% possible obs: 87.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD, MIR / Resolution: 2.5→19.59 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2260688.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 455 5.1 %RANDOM
Rwork0.208 ---
obs0.208 8995 95.3 %-
all-9439 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8891 Å2 / ksol: 0.342283 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.32 Å29.72 Å20 Å2
2--6.32 Å20 Å2
3----12.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-6 Å
Luzzati sigma a0.52 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 26 143 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.532
X-RAY DIFFRACTIONc_mcangle_it2.72.5
X-RAY DIFFRACTIONc_scbond_it2.062.5
X-RAY DIFFRACTIONc_scangle_it3.33
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 61 4.4 %
Rwork0.349 1327 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NUC.PARAMNUC.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SAH.PARAMSAH.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor Rwork: 0.35

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