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- PDB-3bgv: Crystal structure of mRNA cap guanine-N7 methyltransferase in com... -

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Basic information

Entry
Database: PDB / ID: 3bgv
TitleCrystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH
ComponentsmRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / methyltransferase / Alternative splicing / mRNA capping / mRNA processing / Nucleus / Phosphoprotein / RNA-binding / S-adenosyl-L-methionine / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mRNA capping enzyme complex / : / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...mRNA capping enzyme complex / : / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / receptor complex / RNA binding / nucleoplasm / nucleus
Similarity search - Function
mRNA cap guanine-N7 methyltransferase, eukaryotes / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / 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-N7 methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLunin, V.V. / Wu, H. / Zeng, H. / Antoshenko, T. / MacKenzie, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. ...Lunin, V.V. / Wu, H. / Zeng, H. / Antoshenko, T. / MacKenzie, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human RNA (guanine-7-) methyltransferase in complex with SAH.
Authors: Wu, H. / Lunin, V.V. / Zeng, H. / Antoshenko, T. / MacKenzie, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: mRNA cap guanine-N7 methyltransferase
B: mRNA cap guanine-N7 methyltransferase
C: mRNA cap guanine-N7 methyltransferase
D: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,6308
Polymers147,0934
Non-polymers1,5384
Water8,575476
1
A: mRNA cap guanine-N7 methyltransferase


Theoretical massNumber of molelcules
Total (without water)36,7731
Polymers36,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA cap guanine-N7 methyltransferase


Theoretical massNumber of molelcules
Total (without water)36,7731
Polymers36,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: mRNA cap guanine-N7 methyltransferase
hetero molecules


  • defined by author&software
  • 38.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)38,3115
Polymers36,7731
Non-polymers1,5384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: mRNA cap guanine-N7 methyltransferase


Theoretical massNumber of molelcules
Total (without water)36,7731
Polymers36,7731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.787, 99.672, 167.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7)-)-methyltransferase / RG7MT1 / mRNA cap methyltransferase / hcm1p / hCMT1 / hMet


Mass: 36773.211 Da / Num. of mol.: 4 / Fragment: Residues 165-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M KCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792996 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792996 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 58716 / Num. obs: 58716 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.6 % / Rsym value: 0.141 / Net I/σ(I): 27.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 3.35 / Num. unique all: 5774 / Rsym value: 0.698 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RI1

1ri1


Resolution: 2.3→49.51 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.83 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.377 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29448 2942 5.1 %RANDOM
Rwork0.22122 ---
all0.22486 55206 --
obs0.22486 55206 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.903 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2---2.43 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8779 0 104 476 9359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229069
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.98112172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93651067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52724.376425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.133151681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9541543
X-RAY DIFFRACTIONr_chiral_restr0.1180.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026729
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.24147
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26147
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2551
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0741.55604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79828626
X-RAY DIFFRACTIONr_scbond_it2.5734088
X-RAY DIFFRACTIONr_scangle_it3.8254.53545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 229 -
Rwork0.256 3945 -
obs--97.14 %

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