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- PDB-5e9j: Crystal structure of the mRNA cap guanine-N7 methyltransferase - ... -

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Basic information

Entry
Database: PDB / ID: 5e9j
TitleCrystal structure of the mRNA cap guanine-N7 methyltransferase - modular lobe (416-456) deletion
ComponentsmRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / mRNA capping / RNA processing
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 / receptor complex ...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: 3.47 Å
AuthorsPetit, P. / Cowling, V.H.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM.
Authors: Varshney, D. / Petit, A.P. / Bueren-Calabuig, J.A. / Jansen, C. / Fletcher, D.A. / Peggie, M. / Weidlich, S. / Scullion, P. / Pisliakov, A.V. / Cowling, V.H.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Feb 8, 2017Group: Data collection
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,3254
Polymers64,5562
Non-polymers7692
Water00
1
A: mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6632
Polymers32,2781
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6632
Polymers32,2781
Non-polymers3841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.760, 114.380, 134.810
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 cap guanine-N7 methyltransferase / RG7MT1 / mRNA (guanine-N(7)-)-methyltransferase / mRNA cap methyltransferase / hcm1p


Mass: 32278.158 Da / Num. of mol.: 2
Mutation: 416-456(GSGG),416-456(GSGG),416-456(GSGG),416-456(GSGG)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15 / Production host: Escherichia coli (E. coli)
References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1M Hepes pH 7.8, 15% isopropanol and 6% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 2, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3.47→87.21 Å / Num. obs: 13618 / % possible obs: 92.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.21 / Rsym value: 0.19 / Net I/σ(I): 6.6
Reflection shellResolution: 3.47→3.71 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.6 / % possible all: 67.6

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Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BGV

3bgv


Resolution: 3.47→48.806 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 689 5.07 %
Rwork0.2365 --
obs0.238 13580 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.47→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 52 0 4510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034620
X-RAY DIFFRACTIONf_angle_d0.7846194
X-RAY DIFFRACTIONf_dihedral_angle_d15.061735
X-RAY DIFFRACTIONf_chiral_restr0.031644
X-RAY DIFFRACTIONf_plane_restr0.003787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4703-3.73810.4007820.33291909X-RAY DIFFRACTION69
3.7381-4.11410.34741470.29412587X-RAY DIFFRACTION95
4.1141-4.7090.31031430.23242734X-RAY DIFFRACTION99
4.709-5.93120.25751650.23362768X-RAY DIFFRACTION99
5.9312-48.81030.18851520.19422893X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3893-0.68580.53522.2218-1.18424.33-0.2088-0.04150.33990.1848-0.0503-0.1531-0.5673-0.1466-0.00010.7965-0.05220.02610.7352-0.0690.832692.8758133.89135.0849
23.22-0.0087-0.8023.39571.5763.80260.15960.2440.1438-0.2505-0.41410.7291-0.5662-0.6602-0.00030.8443-0.0115-0.05130.9439-0.07140.952970.8079124.6822101.6
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 3:276)
2X-RAY DIFFRACTION2(chain B and resseq 3:276)

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