Single-stranded RNA-mediated PRC2 dimer

2025-10-15 REL RCSB INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.title _citation.year _em_admin.last_update RCSB RCSB 2024-08-26 2025-03-12 2025-03-12 2025-10-15 Howard Hughes Medical Institute (HHMI) United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R00GM132544 United States Single-stranded RNA-mediated PRC2 dimer Song JS Kasinath VK PRC2, RNA, RNP complex, chromatin modifier, GENE REGULATION Song J Yao L Gooding AR Thron V Hemphill WO Goodrich K Kasinath V Cech TR RNA-induced PRC2 inhibition depends on the sequence of bound RNA. Biorxiv US 2025 39257770 doi:10.1101/2024.08.29.610323 2692-8205 EMD-46722 other EM volume

Body1 of TERRAmut RNA-mediated PRC2 dimer

EMD-46726 other EM volume

Body2 of TERRAmut RNA-mediated PRC2 dimer

9dch FULLOVERLAP EMDB EMD-46722 other EM volume

Body1 of TERRAmut RNA-mediated PRC2 dimer

EMDB EMD-46726 other EM volume

Body2 of TERRAmut RNA-mediated PRC2 dimer

EMDB EMD-46751 associated EM volume

Single-stranded RNA-mediated PRC2 dimer

Single-stranded RNA-mediated dimer of Polycomb Repressive Complex 2 Single-stranded RNA-mediated dimer of Polycomb Repressive Complex 2 0 1 2 3 4 5 6 7 dimer of Polycomb Repressive Complex 2 1 2 3 4 5 6 7 Homo sapiens TERRAmut RNA 1 1 Homo sapiens TERRAmut RNA Homo sapiens 0.0032579799999999997 1 UGAGUGUGAG Isoform 2 of Histone-lysine N-methyltransferase EZH2 Homo sapiens 0.08601785899999999 2 Trichoplusia ni LEVO GQTGKKSEKGPVCWRKRVKSEYMRLRQLKRFRRADEVKSMFSSNRQKILERTEILNQEWKQRRIQPVHILTSVSSLRGTR ECSVTSDLDFPTQVIPLKTLNAVASVPIMYSWSPLQQNFMVEDETVLHNIPYMGDEVLDQDGTFIEELIKNYDGKVHGDR ECGFINDEIFVELVNALGQYNDDDDDDDGDDPEEREEKQKDLEDHRDDKESRPPRKFPSDKIFEAISSMFPDKGTAEELK EKYKELTEQQLPGALPPECTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHRKCNYSFHATPNTYKRKNTETALD NKPCGPQCYQHLEGAKEFAAALTAERIKTPPKRPGGRRRGRLPNNSSRPSTPTINVLESKDTDSDREAGTETGGENNDKE EEEKKDETSSSSEANSRCQTPIKMKPNIEPPENVEWSGAEASMFRVLIGTYYDNFCAIARLIGTKTCRQVYEFRVKESSI IAPAPAEDVDTPPRKKKRKHRLWAAHCRKIQLKKDGSSNHVYNYQPCDHPRQPCDSSCPCVIAQNFCEKFCQCSSECQNR FPGCRCKAQCNTKQCPCYLAVRECDPDLCLTCGAADHWDSKNVSCKNCSIQRGSKKHLLLAPSDVAGWGIFIKDPVQKNE FISEYCGEIISQDEADRRGKVYDKYMCSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVMMVNGDHRIGIFAKRAI QTGEELFFDYRYSQADALKYVGIEREMEIP Q15910 2.1.1.356 Polycomb protein SUZ12 Homo sapiens 0.082353133 2 Trichoplusia ni LEVO MAPQKHGGGGGGFGGSAAVAAATASGGKSGGGSCGGGGSYSASSSSSAAAAAGAAVLPVKKPKMEHVQADHELFLQAFEK PTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPS PNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLF RVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEECPISKKRA TWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQT RKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSIN ECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLESEDGEVEQQRTYSSGHNRLYFHSDTCL PLRPQEMEVDSEDEKDPEWLREKTITQIEEFSDVNEGEKEVMKLWNLHVMKHGFIADNQMNHACMLFVENYGQKIIKKNL CRNFMLHLVSMHDFNLISIMSIDKAVTKLREMQQKLEKGESASPANEEITEEQNGTANGFSEINSKEKALETDSVSGVSK QSKKQKL Q15022 RBAP48 Homo sapiens 0.047709527 2 Trichoplusia ni LEVO MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLV IASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSK PDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHE SLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEI FQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQ VWQMAENIYNDEDPEGSVDPEGQGS Q09028 Zinc finger protein AEBP2 Homo sapiens 0.032881472999999994 2 Trichoplusia ni LEVO SSDGEPLSRMDSEDSISSTIMDVDSTISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSSPDLADHIRSIHVDG QRGGVFVCLWKGCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQQNSSKVSSQPKAKE ESPSKAGMNKRRKLKNKRRRSLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKRKEDSGKIKLLL HWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR Q6ZN18 Protein Jumonji Homo sapiens 0.036021391 2 Trichoplusia ni LEVO QSQPNSPSTTPVKIVEPLLPPPATQISDLSKRKPKTEDFLTFLCLRGSPALPNSMVYFGSSQDEEEVEEEDDETEDVKTA TNNASSSCQSTPRKGKTHKHVHNGHVFNGSSRSTREKEPVQKHKSKEATPAKEKHSDHRADSRREQASANHPAAAPSTGS SAKGLAATHHHPPLHRSAQDLRKQVSKVNGVTRMSSLGAGVTSAKKMREVRPSPSKTVKYTATVTKGAVTYTKAKRELVK DTKPNHHKPSSAVNHTISGKTESSNAKTRKQVLSLGGASKSTGPAVNGLKVSGRLNPKSCTKEVGGRQLREGLQLREGLR NSKRRLEEAHQA Q92833 Polycomb protein EED Homo sapiens 0.050267690999999996 2 Trichoplusia ni LEVO MSEREVSTAPAGTDMPAAKKQKLSSDENSNPDLSGDENDDAVSIESGTNTERPDTPTNTPNAPGRKSWGKGKWKSKKCKY SFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSH PLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVL SADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLIL SKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAK CTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR O75530 ZINC ION 6.5409e-05 14 ZN singleParticle particle 7.9

RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1 mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1 mM TCEP) EM preparation buffer II (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, 0.01%NP-40, and 1 mM TCEP).

ETHANE 90 281 LEICA EM GP

2-3s of single side blotting.

We used streptavidin-affinity grid preparation method with biotin-labeled RNA at 100 nM concentration. PRC2 was applied in excess at 600 nM.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 1.9000000000000001 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 2 14230 50.0

Cryo-EM data was collected using a Titan Krios G3i equipped with a Thermo Fisher Falcon 4 direct-electron detector (DED) camera and a Selectris energy filter set with a 10-eV slit width. Data acquisition was performed using Thermo Fisher EPU at 130,000x magnification (0.97 A/pixel) with a defocus range of minus 1.9 to minus 0.5 micrometer. Movies were collected in EER format with a total dose of 50 electrons per square angstrom and an exposure time of 5.49 s corresponding to 1323 frames.

Gain correction was applied during motion correction using Relion own implementation of the UCSF motioncor2 program

3385491

TOPAZ auto picking

RELION 5

CTFind

PHASE FLIPPING AND AMPLITUDE CORRECTION

Negative straining EM model

3.4 FSC 0.143 CUT-OFF RELION 5 120658 MAXIMUM LIKELIHOOD RELION 5 MAXIMUM LIKELIHOOD RELION 5 emd_46751.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 310.40002 310.40002 310.40002 90.0 90.0 90.0 X Y Z -0.015072217 0.04562093 0.00012886216 0.0013691015 0.9700001 0.9700001 0.9700001 0.0052 AUTHOR ::::EMDATABANK.org::::EMD-46751:::: Consensus map of the single-stranded TERRAmut RNA-bound PRC2 dimer 8FYH PDB experimental model

Individual PRC2 protomers were built using cryo-EM maps from the multibody refinement. The coordinates of G-quadruplex RNA-bound PRC2 six-subunit complex (PDB: 8FYH) provided a starting model from which all the coordinates were adjusted and rebuilt in the new map using COOT. The model of each PRC2 promoter was subjected to global refinement and minimization in real space using PHENIX. These were then subjected to manual inspection and adjustment in COOT, followed by refinement again in PHENIX. TERRAmut RNA model was generated using a 10-nucleotide single-stranded fragment (UGAGUGUGAG) using AlphaFold3 and then docked into our map for the position we designated as the RNA density.

emd_46751_msk_1.map emd_46751_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 310.40002 310.40002 310.40002 90.0 90.0 90.0 X Y Z -0.021220783 0.051868774 0.00013407775 0.0017501807 0.9700001 0.9700001 0.9700001 AUTHOR ::::EMDATABANK.org::::EMD-46751:::: emd_46751_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 310.40002 310.40002 310.40002 90.0 90.0 90.0 X Y Z -0.021281758 0.05378139 0.00013589954 0.0017513738 0.9700001 0.9700001 0.9700001 AUTHOR ::::EMDATABANK.org::::EMD-46751::::