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- PDB-5e9w: Crystal structure of mRNA cap guanine-N7 methyltransferase obtain... -

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Basic information

Entry
Database: PDB / ID: 5e9w
TitleCrystal structure of mRNA cap guanine-N7 methyltransferase obtained by limited proteolysis
ComponentsmRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / mRNA capping
Function / homology
Function and homology information


mRNA cap methyltransferase RNMT:RAMAC 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 ...mRNA cap methyltransferase RNMT:RAMAC 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 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.283 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 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jan 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

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)148,4028
Polymers146,8654
Non-polymers1,5384
Water5,531307
1
A: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1012
Polymers36,7161
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.458, 99.157, 167.614
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 / RG7MT1 / mRNA (guanine-N(7)-)-methyltransferase / mRNA cap methyltransferase / hcm1p


Mass: 36716.160 Da / Num. of mol.: 4 / Fragment: UNP residues 165-476
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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES pH 6.5 and 25% PEG 4000, 1/5000 thermolysin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→29.58 Å / Num. obs: 57298 / % possible obs: 97 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.28→2.41 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.9 / % possible all: 97.6

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Processing

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

3bgv


Resolution: 2.283→29.578 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2886 5.05 %
Rwork0.2201 --
obs0.2219 57204 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.283→29.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8989 0 104 307 9400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089297
X-RAY DIFFRACTIONf_angle_d1.34212468
X-RAY DIFFRACTIONf_dihedral_angle_d15.0343544
X-RAY DIFFRACTIONf_chiral_restr0.0571313
X-RAY DIFFRACTIONf_plane_restr0.0071574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2825-2.31990.32871300.27762549X-RAY DIFFRACTION97
2.3199-2.35990.31361470.25772589X-RAY DIFFRACTION98
2.3599-2.40280.33581530.25612548X-RAY DIFFRACTION97
2.4028-2.4490.28031420.24492531X-RAY DIFFRACTION97
2.449-2.4990.30521310.24682616X-RAY DIFFRACTION96
2.499-2.55330.31051440.24512535X-RAY DIFFRACTION97
2.5533-2.61260.29231010.24652631X-RAY DIFFRACTION97
2.6126-2.67790.28021230.2552596X-RAY DIFFRACTION96
2.6779-2.75030.27981420.23252560X-RAY DIFFRACTION97
2.7503-2.83120.24381380.23222580X-RAY DIFFRACTION97
2.8312-2.92250.27941240.23182588X-RAY DIFFRACTION97
2.9225-3.02680.25731560.23422537X-RAY DIFFRACTION96
3.0268-3.14790.27841440.2342596X-RAY DIFFRACTION97
3.1479-3.2910.24691340.22552615X-RAY DIFFRACTION97
3.291-3.46420.2291120.21722619X-RAY DIFFRACTION97
3.4642-3.68090.25051510.20432604X-RAY DIFFRACTION96
3.6809-3.96450.24991300.21272602X-RAY DIFFRACTION97
3.9645-4.36230.24211380.19172611X-RAY DIFFRACTION96
4.3623-4.99090.20031380.17722625X-RAY DIFFRACTION96
4.9909-6.27810.22451500.21122586X-RAY DIFFRACTION94
6.2781-29.58090.21161580.19092600X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 58.1387 Å / Origin y: 64.3557 Å / Origin z: 62.7484 Å
111213212223313233
T0.1216 Å20.011 Å20.0035 Å2-0.0897 Å20.0131 Å2--0.0726 Å2
L0.6064 °20.3329 °20.0389 °2-0.2266 °20.0408 °2--0.0451 °2
S0.0667 Å °-0.0306 Å °0.013 Å °0.0524 Å °-0.0459 Å °0.0152 Å °0.0296 Å °-0.0031 Å °-0.0196 Å °
Refinement TLS groupSelection details: all

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