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- PDB-8q69: Crystal structure of HsRNMT complexed with inhibitor DDD1060606 -

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Basic information

Entry
Database: PDB / ID: 8q69
TitleCrystal structure of HsRNMT complexed with inhibitor DDD1060606
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 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. / 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: 1.96 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 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 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)66,8079
Polymers65,1012
Non-polymers1,7067
Water7,296405
1
A: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3574
Polymers32,5511
Non-polymers8073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4505
Polymers32,5511
Non-polymers8994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.195, 84.574, 81.966
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number4
Space group name H-MP1211

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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, 412 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-K7R / 1-[(3~{S})-3-(2~{H}-pyrazolo[3,4-b]pyridin-3-yl)piperidin-1-yl]-2-thiophen-3-yl-ethanone


Mass: 326.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
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: Y
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 1, 2017
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→42.29 Å / Num. obs: 36929 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.2
Reflection shellResolution: 1.96→2.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4597 / CC1/2: 0.65 / % possible all: 82.9
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→40.47 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2892 1723 4.69 %
Rwork0.2423 --
obs0.2444 36724 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4395 0 114 405 4914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054607
X-RAY DIFFRACTIONf_angle_d0.8986173
X-RAY DIFFRACTIONf_dihedral_angle_d20.001627
X-RAY DIFFRACTIONf_chiral_restr0.047645
X-RAY DIFFRACTIONf_plane_restr0.003772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.020.42361200.42012252X-RAY DIFFRACTION76
2.02-2.080.36851560.36922749X-RAY DIFFRACTION91
2.08-2.160.30561390.28972967X-RAY DIFFRACTION99
2.16-2.240.44611450.33332862X-RAY DIFFRACTION95
2.24-2.340.32331670.28892988X-RAY DIFFRACTION99
2.34-2.470.27481380.25943017X-RAY DIFFRACTION100
2.47-2.620.33821250.27423037X-RAY DIFFRACTION100
2.62-2.820.291620.25072998X-RAY DIFFRACTION100
2.82-3.110.28321450.2483000X-RAY DIFFRACTION100
3.11-3.560.27721360.21383057X-RAY DIFFRACTION100
3.56-4.480.24151350.19342999X-RAY DIFFRACTION99
4.48-40.470.2481550.20793075X-RAY DIFFRACTION100

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