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- PDB-9ay9: Co-crystal structure of human PRMT9 in complex with MRK-990 inhibitor -

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Basic information

Entry
Database: PDB / ID: 9ay9
TitleCo-crystal structure of human PRMT9 in complex with MRK-990 inhibitor
ComponentsProtein arginine N-methyltransferase 9
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Methyltransferase / PRMT9 / SGC / TRANSPORT PROTEIN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity ...type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / histone H2AQ104 methyltransferase activity / histone methyltransferase activity / mRNA processing / methylation / chromatin remodeling / regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L11 methyltransferase (PrmA) / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Protein arginine N-methyltransferase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsZeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. ...Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Co-crystal structure of human PRMT9 in complex with MRK-990 inhibitor
Authors: Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / ...Authors: Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Li, Y. / Gao, Y.D. / Schneider, S. / Siliphaivanh, P. / Sloman, D. / Nicholson, B. / Fischer, C. / Hicks, J. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionMar 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 9
B: Protein arginine N-methyltransferase 9
C: Protein arginine N-methyltransferase 9
D: Protein arginine N-methyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,00410
Polymers321,9454
Non-polymers2,0596
Water10,773598
1
A: Protein arginine N-methyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0012
Polymers80,4861
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein arginine N-methyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0012
Polymers80,4861
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein arginine N-methyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0013
Polymers80,4861
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein arginine N-methyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0013
Polymers80,4861
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.374, 223.078, 84.698
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein arginine N-methyltransferase 9 / Protein arginine N-methyltransferase 10


Mass: 80486.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT9, PRMT10 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6P2P2, type II protein arginine methyltransferase
#2: Chemical
ChemComp-A1AHM / 7-[5-S-(4-{[(2-tert-butylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 514.683 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H38N6O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M Ammonium Nitrate

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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 EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 151743 / % possible obs: 97.9 % / Redundancy: 5.3 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.052 / Rrim(I) all: 0.12 / Χ2: 1.474 / Net I/σ(I): 8 / Num. measured all: 801919
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.22-2.264.60.82975940.5650.850.4290.9381.17598.4
2.26-2.34.60.82575560.5980.8650.4270.9340.93998.2
2.3-2.345.30.66576520.7450.9240.3170.740.90198.5
2.34-2.395.10.54472270.7740.9340.2610.6070.92794.1
2.39-2.445.80.49977080.8510.9590.2290.550.95599.2
2.44-2.560.45577270.8770.9670.2050.50.96999.9
2.5-2.5660.37477550.9090.9760.1680.411.01699.9
2.56-2.6360.32876680.9270.9810.1470.361.04699.9
2.63-2.715.90.27777310.9420.9850.1250.3051.1199.8
2.71-2.85.80.2377250.9580.9890.1040.2531.24199.9
2.8-2.95.80.19377200.9680.9920.0880.2131.33899.8
2.9-3.015.60.15777280.9780.9940.0730.1731.48999.6
3.01-3.155.40.12777150.9810.9950.060.1411.72299.2
3.15-3.325.20.1175960.9840.9960.0530.1221.94498.9
3.32-3.524.60.09175710.9860.9960.0450.1022.11396.6
3.52-3.84.50.08572350.9860.9970.0430.0962.28794
3.8-4.184.70.07773830.9870.9970.0390.0872.46495.4
4.18-4.784.60.06973130.990.9970.0350.0782.4793.7
4.78-6.024.90.06774240.990.9970.0330.0762.34795.4
6.02-505.20.05777150.9940.9980.0270.064298.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→46.58 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1509 0.99 %RANDOM
Rwork0.208 ---
obs0.209 151692 97.4 %-
Displacement parametersBiso mean: 49.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.6103 Å20 Å23.7554 Å2
2--2.3658 Å20 Å2
3----0.7555 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.22→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18610 0 146 598 19354
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0119286HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1126332HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6369SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3295HARMONIC5
X-RAY DIFFRACTIONt_it19286HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion17.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2637SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21530SEMIHARMONIC4
LS refinement shellResolution: 2.22→2.23 Å
RfactorNum. reflection% reflection
Rfree0.3072 -0.89 %
Rwork0.2771 3007 -
obs--76.99 %
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)
10.4322-0.1701-0.23890.55730.2010.7979-0.028-0.1297-0.12870.11340.0090.12650.14890.06840.0191-0.0582-0.0060.0721-0.14770.0211-0.017339.45434.809134.6322
20.7436-0.22010.2130.6312-0.15430.4347-0.0014-0.066-0.1483-0.13350.01960.11740.1239-0.1316-0.0182-0.0168-0.02210.0289-0.1555-0.0075-0.05847.976860.6644-2.5143
30.78870.25750.22870.5654-0.0650.662-0.04810.26520.0387-0.15190.06710.034-0.02390.0734-0.019-0.0756-0.04640.0323-0.11540.0024-0.0987-2.3028-3.951-15.6175
40.64090.0752-0.1740.58290.24750.7892-0.0129-0.06650.0277-0.02730.0642-0.1582-0.04170.2616-0.0513-0.08730.0030.075-0.1386-0.0442-0.0663-26.950351.929340.1513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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