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- PDB-7s0u: PRMT5/MEP50 crystal structure with MTA and phthalazinone fragment... -

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Basic information

Entry
Database: PDB / ID: 7s0u
TitlePRMT5/MEP50 crystal structure with MTA and phthalazinone fragment bound
Components
  • Methylosome protein 50
  • Protein arginine N-methyltransferase 5
KeywordsTRANSFERASE / PRMT5 / MTAP / MTA / methyl transferase / collateral lethality / synthetic lethality / fragment-based lead discovery
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 H4R3 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 H4R3 methyltransferase activity / : / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of mitotic nuclear division / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / E-box binding / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / ubiquitin-like ligase-substrate adaptor activity / 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 / p53 binding / transcription corepressor activity / 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. / Divalent-metal-dependent TIM barrel enzymes / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-(aminomethyl)phthalazin-1(2H)-one / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGunn, R.J. / Thomas, N.C. / Lawson, J.D. / Ivetac, A. / Smith, C.R. / Kulyk, S. / Marx, M.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP -Deleted Cancers.
Authors: Smith, C.R. / Aranda, R. / Bobinski, T.P. / Briere, D.M. / Burns, A.C. / Christensen, J.G. / Clarine, J. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jean-Baptiste, R. / Ketcham, J.M. / ...Authors: Smith, C.R. / Aranda, R. / Bobinski, T.P. / Briere, D.M. / Burns, A.C. / Christensen, J.G. / Clarine, J. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jean-Baptiste, R. / Ketcham, J.M. / Kobayashi, M. / Kuehler, J. / Kulyk, S. / Lawson, J.D. / Moya, K. / Olson, P. / Rahbaek, L. / Thomas, N.C. / Wang, X. / Waters, L.M. / Marx, M.A.
History
DepositionAug 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Structure summary / Category: audit_author / pdbx_database_related
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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 5
B: Methylosome protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2197
Polymers111,6262
Non-polymers5935
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-27 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.748, 138.418, 177.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein Methylosome protein 50 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / p44/Mep50


Mass: 37862.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BQA1

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Non-polymers , 6 types, 137 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-81X / 4-(aminomethyl)phthalazin-1(2H)-one


Mass: 175.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N3O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 100 mM Sodium Citrate pH 5.4, 15% PEG3350, 4% Tascimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 50573 / % possible obs: 74.5 % / Redundancy: 3 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7
Reflection shellResolution: 2.01→2.05 Å / Num. unique obs: 1021 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBQ

4gbq


Resolution: 2.01→44.98 Å / SU ML: 0.2791 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.6221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 2494 4.93 %
Rwork0.2309 48079 -
obs0.2325 50573 62.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.94 Å2
Refinement stepCycle: LAST / Resolution: 2.01→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 39 132 7348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027401
X-RAY DIFFRACTIONf_angle_d0.443610081
X-RAY DIFFRACTIONf_chiral_restr0.04341118
X-RAY DIFFRACTIONf_plane_restr0.0031299
X-RAY DIFFRACTIONf_dihedral_angle_d11.52182672
LS refinement shellResolution: 2.01→2.05 Å
RfactorNum. reflection% reflection
Rfree0.3662 29 -
Rwork0.3417 662 -
obs--25.5 %
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)
11.2105512983-1.06577633094-0.1250108787621.152657121350.2181736665251.06212697182-0.00198533227548-0.0844432052217-0.1564052744230.05088629748610.0459682017189-0.12335071430.5689005837590.706582483225-0.03153886953960.5468368226510.3668520571690.0460904161230.587347003337-0.02662987659990.2999904781-23.8574722278-95.4903723962-17.7448847969
24.42272614567-0.9261226114621.006167644791.87088756011-0.6585710390211.250477529220.0527400548279-0.290622661030.2528265087190.268465063974-0.2308967784350.1516565859770.4184978949410.2942486815990.171714937020.1968149645760.03727450064420.09266949178940.269991170675-0.06125584644350.271773486723-34.3547001979-86.3733856565-17.5042439558
31.15347014119-0.4462019588340.03925112859272.59226127170.6073085234170.2155763009140.2801594480370.186112633625-0.0425269932686-0.736113025987-0.1930029743050.0334372197976-0.04363901336230.287137590959-0.09816088866960.308582692540.2754674782780.03280039348060.435579337014-0.02131479868010.296419255686-31.979566432-79.9501028716-33.4009703161
40.651602181546-0.0179462162177-0.4845349341890.8715774569620.03183749695031.012561801340.1621283558750.3374875720470.198100151739-0.31198606513-0.0584436328912-0.3331594739050.05035870411140.628477617901-0.1441214780780.2284593483980.1106384674440.2207605039420.8206364760370.02871579213560.388861098023-16.5994751918-74.7520331236-32.0207110914
50.3491806706560.0831084492230.5205828771110.6661365974760.2932720838350.8026006228590.112395100249-0.007809019706210.0751877575367-0.2364669577580.050500815654-0.269380349421-0.4144352273140.871081536741-0.1814747130260.474286980835-0.2860636489150.1046593993270.59782626090.02040507708660.369421573353-20.6900219598-56.2003984362-13.145579643
60.435949443592-0.04325725584280.2548152056880.19264092310.2717080471570.9046395621780.030807632006-0.008744649865650.1908167017830.0424662781822-0.00048201741718-0.165324423469-1.087648570770.7302978190970.04322769948870.978177394768-0.5337453807490.06721426994770.3891173470670.0227745255880.338451524462-28.4480181452-31.6630599286-9.74408427222
71.369665777560.8174577223420.06500451101822.900340059340.3073110596481.415503517040.1059745438880.040593311243-0.00129934894588-0.0537184633609-0.1137224096060.157698985667-0.5025582498690.207268307171-0.004822854777550.346282988427-0.07856986203990.005652708430240.1810632882070.004765489344140.131992620435-40.9662993757-51.5372549132-20.3017608904
80.9595907932610.582731472320.1428457346872.11242711726-0.021595206011.063720832760.02037112862490.06452333798180.00630241659616-0.2536457628490.0375034131903-0.0937867944872-0.7029978763520.374015449764-0.03715833270160.295883624758-0.06660731311950.04293644114730.279878835474-0.0008975688667970.175548032888-39.951411913-49.973692777-20.1816163767
90.653696728813-0.126598732612-0.2857254138361.480261912480.8332526869440.543752518244-0.27419688493-0.157648380605-0.3628099465580.4327379676660.188951965264-0.05847202102590.4153041216680.240309367351-0.003697280472791.263986601830.6847828395130.1257986498740.86344409934-0.06974818396280.506528597105-15.965476055-113.479464707-26.8277733999
100.5335800061670.02497568465820.229368373430.561976765507-0.1842109648820.1652235923990.06533216062980.0308057390993-0.1547287898080.02887884115840.0048094639565-0.003844666265490.2643258516260.120006499759-0.06585847947391.485402747320.7904318642920.01205680687681.12798385990.08540942370620.540818587449-12.2435115081-121.749767475-27.4656167045
113.03983777475-0.612383547984-0.1080424399530.1441111651350.2104673659051.70344276933-0.0003495069666410.03622956697140.1125213645350.1204798819940.078300678524-0.1143371435730.2503021280580.0950817817557-0.0729048806881.461459221690.825765010298-0.00916512347051.231775045230.004060120145210.568177769088-8.27372968889-115.076531212-24.8840983264
121.457770966371.06528999554-0.2347055855230.838201510499-0.2383657639050.617279852866-0.207378208120.363668788828-0.346201335743-0.238877193520.215699712515-0.257451022580.1637732398770.113189289942-0.003039489837221.086335567290.634867478980.02998887223651.10071820456-0.1249626577120.422822428922-11.9015477036-111.198626355-37.241044174
130.4370406076260.06427018433030.06049762765430.605821197375-0.08491500625780.0228896058324-0.09496625028380.183523916819-0.426494254718-0.1515216273170.0783032772878-0.660801387350.2327368080480.1901614829420.06375084540280.8541694520570.6444779973880.1144097734581.22644570871-0.07956457159990.693715987803-4.285492855-109.510783266-34.5645910271
140.145732792142-0.211403778295-0.1332707522320.9417948413390.5084740159640.6416312276250.06816971184630.1671217440850.0357024930985-0.290577478647-0.00576074970206-0.3696666599170.2171255763360.556307332533-0.2173911868630.7912338105880.5598473675520.1387246029180.920746339936-0.1165815981210.376260000759-16.2027501423-98.849909397-41.731646306
150.04905135590320.0189400603560.06335347533631.036801123710.5415831316820.4723358178660.03687463764370.03101328207990.0361148633132-0.261408160832-0.0662245624433-0.2241560785110.2045174204160.319846339608-0.07075570165580.9027815465550.4723859602020.1275328312380.652001693743-0.09109428374160.281475610166-25.6343289761-101.86564035-48.0773401198
161.290012115270.425051510536-0.2222045492481.284740635860.007320543914050.04486063167970.07922849440350.514225730402-0.212093587171-0.270391128452-0.149265025064-0.1069610303660.385794200339-0.05783108229720.02480057098671.359483466070.339733775545-0.04528901692940.565886730995-0.09459832952080.349384276326-31.4954716788-105.806171253-47.3168083677
170.900383947345-0.0124375054051-0.06906241092840.855660011207-0.08984479689650.01526243033020.2138292346940.2225982729550.232263813848-0.560772762607-0.1486955545840.205044454875-0.251555666819-0.117332646833-0.01851619762411.350513352920.443491902238-0.03025841464110.53002005127-0.06219432816670.48253129302-35.8822426601-111.420595302-40.9398996095
180.4410172586990.5600479780190.4686621881561.001874905950.8612608206060.743166072801-0.09527246124220.229134265243-0.454893678327-0.06814776547640.01026404836880.2250761103120.3829055289290.131253094740.121083060621.652485941920.326928932619-0.03558352309440.568162746606-0.1394579129270.515374637068-33.9428645801-120.611566805-38.510612338
191.26465291933-0.351320542834-0.2711739297480.7268927366920.1617478134030.07094545535880.03502944751110.123925537178-0.455129496286-0.0740161102854-0.01095478553750.1224208504760.3818999806190.1130761927150.1392750690881.494326835170.628102563532-0.001278458684020.561621725083-0.09184850074150.456012658885-25.6008167748-121.949195824-31.0869213394
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 116 )AA13 - 1161 - 104
22chain 'A' and (resid 117 through 149 )AA117 - 149105 - 137
33chain 'A' and (resid 150 through 208 )AA150 - 208138 - 196
44chain 'A' and (resid 209 through 278 )AA209 - 278197 - 262
55chain 'A' and (resid 279 through 330 )AA279 - 330263 - 308
66chain 'A' and (resid 331 through 487 )AA331 - 487309 - 465
77chain 'A' and (resid 488 through 549 )AA488 - 549466 - 527
88chain 'A' and (resid 550 through 637 )AA550 - 637528 - 614
99chain 'B' and (resid 27 through 55 )BG27 - 551 - 29
1010chain 'B' and (resid 56 through 69 )BG56 - 6930 - 43
1111chain 'B' and (resid 70 through 82 )BG70 - 8244 - 56
1212chain 'B' and (resid 83 through 98 )BG83 - 9857 - 72
1313chain 'B' and (resid 99 through 121 )BG99 - 12173 - 95
1414chain 'B' and (resid 122 through 175 )BG122 - 17596 - 149
1515chain 'B' and (resid 176 through 196 )BG176 - 196150 - 170
1616chain 'B' and (resid 197 through 241 )BG197 - 241171 - 211
1717chain 'B' and (resid 242 through 263 )BG242 - 263212 - 230
1818chain 'B' and (resid 264 through 293 )BG264 - 293231 - 260
1919chain 'B' and (resid 294 through 329 )BG294 - 329261 - 296

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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