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- PDB-9n3r: Crystal structure of PRMT5:MEP50 in complex with MTA and TNG462 -

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Open data


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Basic information

Entry
Database: PDB / ID: 9n3r
TitleCrystal structure of PRMT5:MEP50 in complex with MTA and TNG462
Components
  • Methylosome protein 50
  • Protein arginine N-methyltransferase 5
KeywordsTRANSFERASE/INHIBITOR / inhibitor / MTA-cooperative / MTAP-null / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / 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 / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / histone H2AQ104 methyltransferase activity / endothelial cell activation / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of gene expression via chromosomal CpG island methylation / histone methyltransferase activity / E-box binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / circadian regulation of gene expression / DNA-templated transcription termination / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. ...: / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.47 Å
AuthorsWhittington, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of TNG462: A Highly Potent and Selective MTA-Cooperative PRMT5 Inhibitor to Target Cancers with MTAP Deletion.
Authors: Cottrell, K.M. / Briggs, K.J. / Tsai, A. / Tonini, M.R. / Whittington, D.A. / Gong, S. / Liang, C. / McCarren, P. / Zhang, M. / Zhang, W. / Huang, A. / Maxwell, J.P.
History
DepositionJan 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Protein arginine N-methyltransferase 5
D: Methylosome protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,19015
Polymers223,2524
Non-polymers1,93711
Water1,856103
1
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Protein arginine N-methyltransferase 5
D: Methylosome protein 50
hetero molecules

A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Protein arginine N-methyltransferase 5
D: Methylosome protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,37930
Polymers446,5048
Non-polymers3,87522
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area36210 Å2
ΔGint-193 kcal/mol
Surface area133590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.210, 136.600, 178.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11C-815-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Protein arginine N-methyltransferase 5 / 72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / ...72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / Shk1 kinase-binding protein 1 homolog / SKB1Hs


Mass: 73763.625 Da / Num. of mol.: 2 / Fragment: FULL LENGTH
Source method: isolated from a genetically manipulated source
Details: N-terminal Flag tag / Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein Methylosome protein 50 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / Methylosome protein ...MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / Methylosome protein WDR77 / p44/Mep50


Mass: 37862.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-8 tag / Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BQA1

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Non-polymers , 5 types, 114 molecules

#3: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Chemical ChemComp-A1BV0 / N-(6-amino-5-ethylpyridin-3-yl)-2-{(2R,5S)-5-methyl-2-[2-(1-methylpiperidin-4-yl)-1,3-benzothiazol-5-yl]piperidin-1-yl}-2-oxoacetamide / TNG462


Mass: 520.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H36N6O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride, 1 mM methylthioadenosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.47→29.7 Å / Num. obs: 52173 / % possible obs: 59.4 % / Redundancy: 13.7 % / Biso Wilson estimate: 81.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Net I/σ(I): 13.3
Reflection shellResolution: 2.47→2.54 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 219 / CC1/2: 0.931 / % possible all: 2.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.47→29.7 Å / SU ML: 0.293 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 37.056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 2605 5 %
Rwork0.2099 49523 -
obs0.2116 52128 59.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.31 Å2
Refinement stepCycle: LAST / Resolution: 2.47→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14662 0 127 103 14892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215235
X-RAY DIFFRACTIONf_angle_d0.51220764
X-RAY DIFFRACTIONf_chiral_restr0.04412278
X-RAY DIFFRACTIONf_plane_restr0.00412683
X-RAY DIFFRACTIONf_dihedral_angle_d12.36745506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.511.10960.479583X-RAY DIFFRACTION2.01
2.51-2.560.719460.4392222X-RAY DIFFRACTION5.27
2.56-2.610.3744170.3887382X-RAY DIFFRACTION8.85
2.61-2.670.524330.3494546X-RAY DIFFRACTION12.77
2.67-2.730.3287410.3299768X-RAY DIFFRACTION17.87
2.73-2.80.3263580.32731014X-RAY DIFFRACTION23.76
2.8-2.870.3536720.32861370X-RAY DIFFRACTION31.73
2.87-2.960.3644920.3651893X-RAY DIFFRACTION43.84
2.96-3.050.39761170.32872436X-RAY DIFFRACTION56.28
3.05-3.160.31621470.29362881X-RAY DIFFRACTION66.75
3.16-3.290.32831630.29183343X-RAY DIFFRACTION76.95
3.29-3.440.30172340.28433813X-RAY DIFFRACTION88.4
3.44-3.620.28492110.24334272X-RAY DIFFRACTION98.14
3.62-3.840.28392310.22164334X-RAY DIFFRACTION99.93
3.85-4.140.2592280.20024385X-RAY DIFFRACTION99.89
4.14-4.560.20472230.17054362X-RAY DIFFRACTION99.96
4.56-5.210.19752350.16334417X-RAY DIFFRACTION99.96
5.21-6.560.23462420.20924395X-RAY DIFFRACTION99.36
6.56-29.70.20142490.18554607X-RAY DIFFRACTION99.65
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)
12.13156043337-0.181779572508-0.1754020372732.32560091540.1074774900551.580515609-0.1250477048780.182841287520.3231641218170.1538547166950.128261989792-0.302479385746-0.0955610651970.3987997315080.02317093954880.61318003994-0.102512796516-0.1103850736420.639936193329-0.04958837239180.55752770701921.92447476524.369375038462.4153561935
21.451469875610.263095528177-0.2553713749341.095444382750.5648916297161.62826775081-0.018505839421-0.210072862918-0.05547660062910.5480758277960.0979042845681-0.3727631807-0.02310642423720.725722017423-0.04999547348560.769514736737-0.0693294270897-0.2064489878940.770363536244-0.0458653741920.71975099141825.69614359469.2952694493877.8693135476
30.003627597312440.2249179794330.01222789333771.710029662420.06093316730810.3781835546910.1081713120080.119129666738-0.1277363848580.4554025627140.226065450367-0.8434722304620.257071916680.562781061874-0.2292283381020.657519392840.134856961074-0.1306335801050.997706147019-0.06508606636240.90149276645830.7172939385-10.740389701758.6806584962
41.44501656394-0.587505285462-0.2935178808112.343423233990.4194966730271.74530103254-0.0511637984983-0.171922581862-0.1374929470950.2834489376790.0736526942031-0.2472811552940.6300244635650.40654017523-0.03523083903980.7386619954140.123941780699-0.0919777054670.6393692061150.03622190748630.55245404690516.7962233555-27.142250342759.6121235622
50.9252529471140.8122194017450.3188900432750.8788659388240.1313321393651.610752396140.625166360774-0.08284463288790.1805830230690.478819785501-0.255944886209-0.679934889112-0.4234407303450.348655658-0.1344200135971.16348552253-0.300628091869-0.1739570820850.986884449817-0.1276659512311.0876327647733.9133301448.443823405171.1014426319
60.89492829868-0.266382966624-0.3792376922420.734228299923-0.8977580154492.119375404440.144813202686-0.105003902783-0.3031168543870.349662685023-0.0360880551302-0.583099876324-0.1408255639610.383168396841-0.02179295670161.15145125973-0.224591949079-0.3180311312530.899615053273-0.1266819005430.85496114117532.632342240135.602848738685.3797243082
71.2930427474-1.03092193730.2008212110021.29432836038-0.1708082903790.2286057147960.0844720368372-0.6263504954570.1183532409580.721445383779-0.08474356414430.290221071360.133447332095-0.5175024760730.04059590352921.3937321823-0.176022319907-0.1146224043630.864337560101-0.09227528804150.84971638644214.336595089539.028527243589.977107107
81.249896444160.187232147424-0.5152401473921.37515261327-0.4527247875090.88415556608-0.0144713775399-0.09740619679190.576087621270.05144515620960.154050785254-0.170345949978-0.848410445005-0.216687167697-0.1043433610141.34348869963-0.102086576514-0.1811652767590.848970696541-0.1055658622190.91445506922917.8869365353.025478008878.5002558873
92.27512641833-0.191001098910.597722273022.25084374964-0.01948535704042.235735144010.0256070575776-0.156631984714-0.108317299163-0.07043033884640.0295235238325-0.3884187781460.3569271942860.585201427049-0.08560976199820.4694507379790.1257928650640.0658382885370.625851156106-0.06951002964670.56091614019424.3132538177-22.052126003626.6381477636
102.32361699675-0.2864962131790.554641644951.661048999060.9885743745421.504701891480.1265076888610.1237271435060.080574901729-0.483930805080.0872832661467-0.245416949024-0.330560679770.576332688333-0.1413037326550.507939250402-0.02665133676050.1888364403590.637397050615-0.03555229542770.65061377832626.2415260684-6.8214688604210.9833987637
110.02854347458620.2425483809150.006065953676531.589572045260.5324146704530.130416180880.0268742166706-0.151049966831-0.0446435765988-0.1175802892390.149237142724-0.888026181276-0.1629248470080.682714029957-0.1153068236820.674527301001-0.220744721540.0946065830260.977654964451-0.06763806244770.89601530281729.448714726313.843316447830.1363587551
120.888297859270.3671297130140.463845469722.408514325330.5719814486451.4709590358-0.01148442995760.05792715339180.138427592549-0.1394922405440.0215797420881-0.263466433661-0.5106385107890.379711630752-0.003568237286310.552457705342-0.1277245771830.06616275146560.5664123941220.01306261510890.53716854276413.929302722328.804596533629.2935425875
130.79313968784-0.0191265375573-0.8391042950763.620294747592.254340826182.355750286330.4771781474950.1387091170230.2590797117170.884356485463-0.2376182739-1.192834922051.322588695711.1659761545-0.3356576808461.334357521310.6106736804580.06388298970791.29913096416-0.0624612353031.0954804625639.2953326755-44.298952674417.970950109
140.8398404810970.5475553882340.5597244254971.16443642333-0.4491557422741.01679278755-0.0991449394409-0.0192878160873-0.0889492630984-0.07273843951190.106191388078-0.5393799209790.6080966625970.7154434860760.05623177737210.8574775953550.3625098112720.08885460770451.00849341876-0.106087770360.73357181207536.3826187829-31.6904526943.58901885075
151.891897210951.08563842162-0.9616647349931.50825499913-0.2082463400291.92101331466-0.03643117738410.6446127745790.0809558123117-0.4245777701440.1225550483790.427356882530.927406685118-0.495550210904-0.1204726935271.093252813070.2645405068740.01215722663610.813627930847-0.02342502063550.74742924300618.1318295034-37.0518091394-1.09294957322
160.931590345721-1.012316535440.1567333934631.06347952931-0.1256283396460.04921840789630.2733034143910.151077660221-0.5616743298250.2898207348660.0871787951897-0.2870713059432.00166737210.486766870628-0.2996039172641.621681486720.390901870426-0.06638498569620.789325616588-0.09434380999090.8004856275824.0320361185-50.79065646410.3613245256
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 156 )AA13 - 1561 - 144
22chain 'A' and (resid 157 through 277 )AA157 - 277145 - 265
33chain 'A' and (resid 278 through 330 )AA278 - 330266 - 318
44chain 'A' and (resid 331 through 637 )AA331 - 637319 - 625
55chain 'B' and (resid 28 through 82 )BB28 - 821 - 55
66chain 'B' and (resid 83 through 196 )BB83 - 19656 - 169
77chain 'B' and (resid 197 through 263 )BB197 - 263170 - 232
88chain 'B' and (resid 264 through 328 )BB264 - 328233 - 297
99chain 'C' and (resid 13 through 156 )CC13 - 1561 - 144
1010chain 'C' and (resid 157 through 277 )CC157 - 277145 - 265
1111chain 'C' and (resid 278 through 330 )CC278 - 330266 - 318
1212chain 'C' and (resid 331 through 637 )CC331 - 637319 - 625
1313chain 'D' and (resid 27 through 82 )DD27 - 821 - 56
1414chain 'D' and (resid 83 through 196 )DD83 - 19657 - 170
1515chain 'D' and (resid 197 through 263 )DD197 - 263171 - 237
1616chain 'D' and (resid 264 through 328 )DD264 - 328238 - 302

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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