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- PDB-8q8g: Crystal structure of HsRNMT complexed with inhibitor DDD1870799 -

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Basic information

Entry
Database: PDB / ID: 8q8g
TitleCrystal structure of HsRNMT complexed with inhibitor DDD1870799
ComponentsmRNA cap guanine-N7 methyltransferase
KeywordsRNA BINDING PROTEIN / Methyl transferase
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 (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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / mRNA cap guanine-N7 methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPetit, A.P. / Fyfe, P.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: To Be Published
Title: Structure-Guided Design of HsRNMT inhibitors
Authors: Petit, A.P. / Fyfe, P.K.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,05111
Polymers65,1012
Non-polymers1,9509
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.977, 84.336, 81.990
Angle α, β, γ (deg.)90.000, 96.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32550.559 Da / Num. of mol.: 2 / Mutation: 416-455 GLGC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O94 / 2-(4-fluorophenyl)-1-[(3~{S})-3-(6-oxidanyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)piperidin-1-yl]ethanone


Mass: 354.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.3-6.9, 50 mM Na2SO4, 18-25 % PEG 6000
PH range: 6.3-6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 12, 2018
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→42.17 Å / Num. obs: 21196 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.156 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2207 / CC1/2: 0.57 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.17 Å / SU ML: 0.3525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1028 4.86 %RANDOM
Rwork0.1958 20144 --
obs0.1989 21172 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 131 108 4661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824648
X-RAY DIFFRACTIONf_angle_d1.01226232
X-RAY DIFFRACTIONf_chiral_restr0.051645
X-RAY DIFFRACTIONf_plane_restr0.0081779
X-RAY DIFFRACTIONf_dihedral_angle_d7.265638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.34171410.24582857X-RAY DIFFRACTION99.87
2.53-2.680.34251550.24312859X-RAY DIFFRACTION99.8
2.68-2.890.28211490.22512876X-RAY DIFFRACTION99.77
2.89-3.180.31781500.21392851X-RAY DIFFRACTION99.9
3.18-3.640.2651470.19292887X-RAY DIFFRACTION99.93
3.64-4.590.23051600.16322856X-RAY DIFFRACTION99.77
4.59-42.170.19171260.17672958X-RAY DIFFRACTION99.64

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