[English] 日本語
Yorodumi
- EMDB-46722: Body 1 from multibody refinement of the single-stranded TERRAmut ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46722
TitleBody 1 from multibody refinement of the single-stranded TERRAmut RNA-bound PRC2 dimer
Map dataBody001 from multibody refinement of the single-stranded TERRAmut RNA-bound PRC2 dimer
Sample
  • Complex: Single-stranded RNA-mediated dimer of polycomb repressive complex 2
    • Protein or peptide: Histone-lysine N-methyltransferase EZH2
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Zinc finger protein AEBP2
    • Protein or peptide: Protein Jumonji JARID2
KeywordsPRC2 / RNA / RNP complex / chromatin modifier / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJiarui JS / Vignesh VK
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM132544 United States
CitationJournal: bioRxiv / Year: 2025
Title: RNA-induced PRC2 inhibition depends on the sequence of bound RNA.
Authors: Jiarui Song / Liqi Yao / Anne R Gooding / Valentin Thron / Wayne O Hemphill / Karen Goodrich / Vignesh Kasinath / Thomas R Cech
Abstract: Methyltransferase PRC2 (Polycomb Repressive Complex 2) deposits histone H3K27 trimethylation to establish and maintain epigenetic gene silencing. PRC2 is precisely regulated by accessory proteins, ...Methyltransferase PRC2 (Polycomb Repressive Complex 2) deposits histone H3K27 trimethylation to establish and maintain epigenetic gene silencing. PRC2 is precisely regulated by accessory proteins, histone post-translational modifications and, particularly, RNA. Research on PRC2-associated RNA has mostly focused on the tight-binding G-quadruplex (G4) RNAs, which inhibit PRC2 enzymatic activity in vitro and in cells, a mechanism explained by our recent cryo-EM structure showing G4 RNA-mediated PRC2 dimerization. However, PRC2 binds a wide variety of RNA sequences, and it remains unclear how diverse RNAs beyond G4 associate with and regulate PRC2. Here, we show that variations in RNA sequence elicit distinct effects on PRC2 function. A single-stranded G-rich RNA and an atypical G4 structure called a pUG-fold mediate PRC2 dimerization nearly identical to that induced by G4 RNA. In contrast, pyrimidine-rich RNAs, including a motif identified by CLIPseq in cells, do not induce PRC2 dimerization and instead bind PRC2 monomers with retention of methyltransferase activity. Only RNAs that dimerize PRC2 compete with nucleosome binding and inhibit PRC2 methyltransferase activity. CRISPR-dCas9 was adapted to localize different RNA elements onto a PRC2-targeted gene, revealing RNA sequence specificity for PRC2 regulation in cells. Thus, PRC2 binds many different RNAs with similar affinity, however, the functional effect on enzymatic activity depends entirely on the sequence of the bound RNA, a conclusion potentially applicable to any RNA- binding protein with a large transcriptome.
History
DepositionAug 23, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46722.png

Downloads & links

-
Map

FileDownload / File: emd_46722.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody001 from multibody refinement of the single-stranded TERRAmut RNA-bound PRC2 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0052
Minimum - Maximum-0.0161537 - 0.05327489
Average (Standard dev.)0.0001057541 (±0.001141899)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 310.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_46722_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_46722_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_46722_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Single-stranded RNA-mediated dimer of polycomb repressive complex 2

EntireName: Single-stranded RNA-mediated dimer of polycomb repressive complex 2
Components
  • Complex: Single-stranded RNA-mediated dimer of polycomb repressive complex 2
    • Protein or peptide: Histone-lysine N-methyltransferase EZH2
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: Zinc finger protein AEBP2
    • Protein or peptide: Protein Jumonji JARID2

-
Supramolecule #1: Single-stranded RNA-mediated dimer of polycomb repressive complex 2

SupramoleculeName: Single-stranded RNA-mediated dimer of polycomb repressive complex 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Histone-lysine N-methyltransferase EZH2

MacromoleculeName: Histone-lysine N-methyltransferase EZH2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GQTGKKSEKG PVCWRKRVKS EYMRLRQLKR FRRADEVKSM FSSNRQKILE RTEILNQEWK QRRIQPVHIL TSVSSLRGTR ECSVTSDLDF PTQVIPLKTL NAVASVPIMY SWSPLQQNFM VEDETVLHNI PYMGDEVLDQ DGTFIEELIK NYDGKVHGDR ECGFINDEIF ...String:
GQTGKKSEKG PVCWRKRVKS EYMRLRQLKR FRRADEVKSM FSSNRQKILE RTEILNQEWK QRRIQPVHIL TSVSSLRGTR ECSVTSDLDF PTQVIPLKTL NAVASVPIMY SWSPLQQNFM VEDETVLHNI PYMGDEVLDQ DGTFIEELIK NYDGKVHGDR ECGFINDEIF VELVNALGQY NDDDDDDDGD DPEEREEKQK DLEDHRDDKE SRPPRKFPSD KIFEAISSMF PDKGTAEELK EKYKELTEQQ LPGALPPECT PNIDGPNAKS VQREQSLHSF HTLFCRRCFK YDCFLHRKCN YSFHATPNTY KRKNTETALD NKPCGPQCYQ HLEGAKEFAA ALTAERIKTP PKRPGGRRRG RLPNNSSRPS TPTINVLESK DTDSDREAGT ETGGENNDKE EEEKKDETSS SSEANSRCQT PIKMKPNIEP PENVEWSGAE ASMFRVLIGT YYDNFCAIAR LIGTKTCRQV YEFRVKESSI IAPAPAEDVD TPPRKKKRKH RLWAAHCRKI QLKKDGSSNH VYNYQPCDHP RQPCDSSCPC VIAQNFCEKF CQCSSECQNR FPGCRCKAQC NTKQCPCYLA VRECDPDLCL TCGAADHWDS KNVSCKNCSI QRGSKKHLLL APSDVAGWGI FIKDPVQKNE FISEYCGEII SQDEADRRGK VYDKYMCSFL FNLNNDFVVD ATRKGNKIRF ANHSVNPNCY AKVMMVNGDH RIGIFAKRAI QTGEELFFDY RYSQADALKY VGIEREMEIP

-
Macromolecule #2: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPQKHGGGG GGFGGSAAVA AATASGGKSG GGSCGGGGSY SASSSSSAAA AAGAAVLPVK KPKMEHVQAD HELFLQAFEK PTQIYRFLRT RNLIAPIFLH RTLTYMSHRN SRTNIKRKTF KVDDMLSKVE KMKGEQESHS LSAHLQLTFT GFFHKNDKPS PNSENEQNSV ...String:
MAPQKHGGGG GGFGGSAAVA AATASGGKSG GGSCGGGGSY SASSSSSAAA AAGAAVLPVK KPKMEHVQAD HELFLQAFEK PTQIYRFLRT RNLIAPIFLH RTLTYMSHRN SRTNIKRKTF KVDDMLSKVE KMKGEQESHS LSAHLQLTFT GFFHKNDKPS PNSENEQNSV TLEVLLVKVC HKKRKDVSCP IRQVPTGKKQ VPLNPDLNQT KPGNFPSLAV SSNEFEPSNS HMVKSYSLLF RVTRPGRREF NGMINGETNE NIDVNEELPA RRKRNREDGE KTFVAQMTVF DKNRRLQLLD GEYEVAMQEM EECPISKKRA TWETILDGKR LPPFETFSQG PTLQFTLRWT GETNDKSTAP IAKPLATRNS ESLHQENKPG SVKPTQTIAV KESLTTDLQT RKEKDTPNEN RQKLRIFYQF LYNNNTRQQT EARDDLHCPW CTLNCRKLYS LLKHLKLCHS RFIFNYVYHP KGARIDVSIN ECYDGSYAGN PQDIHRQPGF AFSRNGPVKR TPITHILVCR PKRTKASMSE FLESEDGEVE QQRTYSSGHN RLYFHSDTCL PLRPQEMEVD SEDEKDPEWL REKTITQIEE FSDVNEGEKE VMKLWNLHVM KHGFIADNQM NHACMLFVEN YGQKIIKKNL CRNFMLHLVS MHDFNLISIM SIDKAVTKLR EMQQKLEKGE SASPANEEIT EEQNGTANGF SEINSKEKAL ETDSVSGVSK QSKKQKL

-
Macromolecule #3: Polycomb protein EED

MacromoleculeName: Polycomb protein EED / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLKE DHNQPLFGVQ FNWHSKEGDP LVFATVGSNR VTLYECHSQG EIRLLQSYVD ADADENFYTC AWTYDSNTSH PLLAVAGSRG ...String:
MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLKE DHNQPLFGVQ FNWHSKEGDP LVFATVGSNR VTLYECHSQG EIRLLQSYVD ADADENFYTC AWTYDSNTSH PLLAVAGSRG IIRIINPITM QCIKHYVGHG NAINELKFHP RDPNLLLSVS KDHALRLWNI QTDTLVAIFG GVEGHRDEVL SADYDLLGEK IMSCGMDHSL KLWRINSKRM MNAIKESYDY NPNKTNRPFI SQKIHFPDFS TRDIHRNYVD CVRWLGDLIL SKSCENAIVC WKPGKMEDDI DKIKPSESNV TILGRFDYSQ CDIWYMRFSM DFWQKMLALG NQVGKLYVWD LEVEDPHKAK CTTLTHHKCG AAIRQTSFSR DSSILIAVCD DASIWRWDRL R

-
Macromolecule #4: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPNDD AQFDASHYDS EKGEFGGFGS VSGKIEIEIK INHEGEVNRA RYMPQNPCII ATKTPSSDVL VFDYTKHPSK PDPSGECNPD ...String:
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPNDD AQFDASHYDS EKGEFGGFGS VSGKIEIEIK INHEGEVNRA RYMPQNPCII ATKTPSSDVL VFDYTKHPSK PDPSGECNPD LRLRGHQKEG YGLSWNPNLS GHLLSASDDH TICLWDISAV PKEGKVVDAK TIFTGHTAVV EDVSWHLLHE SLFGSVADDQ KLMIWDTRSN NTSKPSHSVD AHTAEVNCLS FNPYSEFILA TGSADKTVAL WDLRNLKLKL HSFESHKDEI FQVQWSPHNE TILASSGTDR RLNVWDLSKI GEEQSPEDAE DGPPELLFIH GGHTAKISDF SWNPNEPWVI CSVSEDNIMQ VWQMAENIYN DEDPEGSVDP EGQGS

-
Macromolecule #5: Zinc finger protein AEBP2

MacromoleculeName: Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SSDGEPLSRM DSEDSISSTI MDVDSTISSG RSTPAMMNGQ GSTTSSSKNI AYNCCWDQCQ ACFNSSPDLA DHIRSIHVDG QRGGVFVCLW KGCKVYNTPS TSQSWLQRHM LTHSGDKPFK CVVGGCNASF ASQGGLARHV PTHFSQQNSS KVSSQPKAKE ESPSKAGMNK ...String:
SSDGEPLSRM DSEDSISSTI MDVDSTISSG RSTPAMMNGQ GSTTSSSKNI AYNCCWDQCQ ACFNSSPDLA DHIRSIHVDG QRGGVFVCLW KGCKVYNTPS TSQSWLQRHM LTHSGDKPFK CVVGGCNASF ASQGGLARHV PTHFSQQNSS KVSSQPKAKE ESPSKAGMNK RRKLKNKRRR SLPRPHDFFD AQTLDAIRHR AICFNLSAHI ESLGKGHSVV FHSTVIAKRK EDSGKIKLLL HWMPEDILPD VWVNESERHQ LKTKVVHLSK LPKDTALLLD PNIYRTMPQK RLKR

-
Macromolecule #6: Protein Jumonji JARID2

MacromoleculeName: Protein Jumonji JARID2 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: QSQPNSPSTT PVKIVEPLLP PPATQISDLS KRKPKTEDFL TFLCLRGSPA LPNSMVYFGS SQDEEEVEEE DDETEDVKTA TNNASSSCQS TPRKGKTHKH VHNGHVFNGS SRSTREKEPV QKHKSKEATP AKEKHSDHRA DSRREQASAN HPAAAPSTGS SAKGLAATHH ...String:
QSQPNSPSTT PVKIVEPLLP PPATQISDLS KRKPKTEDFL TFLCLRGSPA LPNSMVYFGS SQDEEEVEEE DDETEDVKTA TNNASSSCQS TPRKGKTHKH VHNGHVFNGS SRSTREKEPV QKHKSKEATP AKEKHSDHRA DSRREQASAN HPAAAPSTGS SAKGLAATHH HPPLHRSAQD LRKQVSKVNG VTRMSSLGAG VTSAKKMREV RPSPSKTVKY TATVTKGAVT YTKAKRELVK DTKPNHHKPS SAVNHTISGK TESSNAKTRK QVLSLGGASK STGPAVNGLK VSGRLNPKSC TKEVGGRQLR EGLQLREGLR NSKRRLEEAH QA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
Details: RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1mM TCEP) EM preparation ...Details: RNP complex buffer (25 mM HEPES pH 7.9, 50 mM KCl, 2 mM MgCl2, 10% glycerol, and 1mM TCEP) EM preparation buffer I (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, and 1mM TCEP) EM preparation buffer II (25 mM HEPES pH 7.9, 50 mM KCl, 2.5% glycerol, 0.01%NP-40, and 1mM TCEP).
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA PLUNGER / Details: 2-3s of single side blotting.
DetailsWe used streptavidin-affinity grid preparation method with biotin-labeled RNA at 100 nM concentration. PRC2 was applied in excess at 600 nM.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 14230 / Average electron dose: 50.0 e/Å2
Details: Cryo-EM data was collected using a Titan Krios G3i equipped with a Thermo Fisher Falcon 4 direct-electron detector (DED) camera and Selectris energy filter. Data acquisition was performed ...Details: Cryo-EM data was collected using a Titan Krios G3i equipped with a Thermo Fisher Falcon 4 direct-electron detector (DED) camera and Selectris energy filter. 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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsGain correction was applied during motion correction using Relion own implementation of the UCSF motioncor2 program.
Particle selectionNumber selected: 3385491
CTF correctionSoftware - Name: RELION (ver. 5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Negative staining model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 120658
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more