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- PDB-6ogn: Crystal structure of mouse protein arginine methyltransferase 7 i... -

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Basic information

Entry
Database: PDB / ID: 6ogn
TitleCrystal structure of mouse protein arginine methyltransferase 7 in complex with SGC8158 chemical probe
ComponentsProtein arginine N-methyltransferase 7
KeywordsTRANSFERASE / PRMT7 / SGC8158 / chemical probe / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


type III protein arginine methyltransferase / protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / histone H4R3 methyltransferase activity / RMTs methylate histone arginines / genomic imprinting / S-adenosylmethionine-dependent methyltransferase activity / spliceosomal snRNP assembly ...type III protein arginine methyltransferase / protein-arginine omega-N monomethyltransferase activity / histone H4 methyltransferase activity / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / histone H4R3 methyltransferase activity / RMTs methylate histone arginines / genomic imprinting / S-adenosylmethionine-dependent methyltransferase activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / fibrillar center / histone binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...Protein arginine N-methyltransferase PRMT7 / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-MJ7 / Protein arginine N-methyltransferase 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsHalabelian, L. / Dong, A. / Zeng, H. / Li, Y. / Hutchinson, A. / Seitova, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat Commun / Year: 2020
Title: Pharmacological inhibition of PRMT7 links arginine monomethylation to the cellular stress response.
Authors: Szewczyk, M.M. / Ishikawa, Y. / Organ, S. / Sakai, N. / Li, F. / Halabelian, L. / Ackloo, S. / Couzens, A.L. / Eram, M. / Dilworth, D. / Fukushi, H. / Harding, R. / Dela Sena, C.C. / Sugo, T. ...Authors: Szewczyk, M.M. / Ishikawa, Y. / Organ, S. / Sakai, N. / Li, F. / Halabelian, L. / Ackloo, S. / Couzens, A.L. / Eram, M. / Dilworth, D. / Fukushi, H. / Harding, R. / Dela Sena, C.C. / Sugo, T. / Hayashi, K. / McLeod, D. / Zepeda, C. / Aman, A. / Sanchez-Osuna, M. / Bonneil, E. / Takagi, S. / Al-Awar, R. / Tyers, M. / Richard, S. / Takizawa, M. / Gingras, A.C. / Arrowsmith, C.H. / Vedadi, M. / Brown, P.J. / Nara, H. / Barsyte-Lovejoy, D.
History
DepositionApr 3, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionApr 17, 2019ID: 6NPG
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9536
Polymers78,3911
Non-polymers2,5625
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.813, 97.813, 169.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein arginine N-methyltransferase 7 / Histone-arginine N-methyltransferase PRMT7 / [Myelin basic protein]-arginine N-methyltransferase PRMT7


Mass: 78391.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt7, Kiaa1933 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q922X9, type III protein arginine methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MJ7 / 5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl)methyl]amino}butyl)-5'-thioadenosine


Mass: 555.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31ClN6O3S
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 647.004 Da / Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 % / Mosaicity: 0.418 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 20% PEG3350, 0.04 M citric acid, 0.06 M Bis-Tris propane, pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2019
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33363 / % possible obs: 99.7 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Rrim(I) all: 0.118 / Χ2: 1.919 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4412.21.17216220.6890.3461.2230.61100
2.44-2.4913.40.98416350.8050.2771.0230.628100
2.49-2.5313.60.82516440.8380.230.8570.673100
2.53-2.5913.90.70216430.8830.1930.7290.715100
2.59-2.6413.80.5716150.9110.1570.5910.815100
2.64-2.713.60.50216530.9310.140.5220.873100
2.7-2.7713.50.41216480.950.1150.4281.019100
2.77-2.8513.40.3416480.9640.0950.3541.159100
2.85-2.9313.20.28816660.9760.0820.31.402100
2.93-3.02130.24216520.9780.0690.2511.68100
3.02-3.1312.70.2116440.980.0610.2192.047100
3.13-3.2612.20.18716620.9870.0550.1962.354100
3.26-3.4110.70.16216540.9870.0510.172.87798.9
3.41-3.5811.50.14316430.990.0440.1493.30498.6
3.58-3.8113.50.13216770.9940.0370.1373.248100
3.81-4.113.60.11616960.9950.0320.1213.37899.9
4.1-4.5213.30.10716830.9940.030.1113.393100
4.52-5.17130.10117180.9950.0280.1053.3299.7
5.17-6.5111.40.09317300.9950.0280.0972.97299.3
6.51-50120.07218300.9860.0220.0752.32997.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4C4A

4c4a


Resolution: 2.4→47.03 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.213 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26122 1632 5 %RANDOM
Rwork0.20849 ---
obs0.2111 31243 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 42 42 4786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134870
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174301
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6346645
X-RAY DIFFRACTIONr_angle_other_deg1.181.5749960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78622.222225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79815725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381526
X-RAY DIFFRACTIONr_chiral_restr0.0550.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9616.9522463
X-RAY DIFFRACTIONr_mcbond_other5.966.952461
X-RAY DIFFRACTIONr_mcangle_it8.27310.43068
X-RAY DIFFRACTIONr_mcangle_other8.27210.4033069
X-RAY DIFFRACTIONr_scbond_it5.8447.1482407
X-RAY DIFFRACTIONr_scbond_other5.8477.152405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.93710.5883575
X-RAY DIFFRACTIONr_long_range_B_refined10.50978.4285033
X-RAY DIFFRACTIONr_long_range_B_other10.51478.4575025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 117 -
Rwork0.327 2250 -
obs--100 %

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