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- EMDB-41146: PRC2-J119-450 monomer bound to H1-nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-41146
TitlePRC2-J119-450 monomer bound to H1-nucleosome
Map dataPRC-J119-450 monomer bound to H1-nucleosome, non-uniform refinement
Sample
  • Complex: PRC2-J119-450 monomer bound to H1-nucleosome
    • Complex: Nucleosome
      • Protein or peptide: x 6 types
      • DNA: x 2 types
    • Complex: PRC2
      • Protein or peptide: x 5 types
  • Ligand: x 1 types
KeywordsHistone methyl transferase / gene repression / epigenetics / chromatin / GENE REGULATION
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / negative regulation of keratinocyte differentiation / CAF-1 complex ...protein localization to pericentric heterochromatin / hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / negative regulation of keratinocyte differentiation / CAF-1 complex / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / ubiquitin-modified histone reader activity / response to tetrachloromethane / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / cerebellar cortex development / random inactivation of X chromosome / primary miRNA binding / regulatory ncRNA-mediated heterochromatin formation / histone H3K27 methyltransferase activity / facultative heterochromatin formation / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / positive regulation of cell cycle G1/S phase transition / positive regulation of transcription regulatory region DNA binding / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of DNA recombination / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / chromatin silencing complex / regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / RSC-type complex / negative regulation of stem cell differentiation / Apoptosis induced DNA fragmentation / Transcription of E2F targets under negative control by DREAM complex / pronucleus / cardiac muscle hypertrophy in response to stress / Polo-like kinase mediated events / synaptic transmission, GABAergic / chromosome condensation / positive regulation of dendrite development / histone H3 methyltransferase activity / cardiac muscle cell proliferation / lncRNA binding / histone methyltransferase complex / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / G1 to G0 transition / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / ATPase complex / histone methyltransferase activity / Sin3-type complex / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / minor groove of adenine-thymine-rich DNA binding / histone deacetylase complex / negative regulation of cell differentiation / G0 and Early G1 / nucleosome binding / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / pericentric heterochromatin / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of epithelial to mesenchymal transition / Cyclin A:Cdk2-associated events at S phase entry / spleen development / keratinocyte differentiation / Deposition of new CENPA-containing nucleosomes at the centromere / protein localization to chromatin / Regulation of TP53 Activity through Acetylation / nucleosomal DNA binding / enzyme activator activity / transcription repressor complex / methylated histone binding / SUMOylation of chromatin organization proteins / B cell differentiation / liver development / positive regulation of GTPase activity / transcription corepressor binding / thymus development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / ubiquitin binding / Regulation of endogenous retroelements by KRAB-ZFP proteins
Similarity search - Function
: / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain ...: / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Linker histone H1/H5 / : / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / JmjC domain, hydroxylase / SANT/Myb domain / A domain family that is part of the cupin metalloenzyme superfamily. / zinc finger / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Polycomb protein EED / Histone H2B 1.1 / Histone H2A type 1 / Histone H1.0 / Histone H4 / Histone H3.2 / Histone-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Zinc finger protein AEBP2 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSauer PV / Cookis T / Pavlenko E / Nogales E / Poepsel S
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol Cell / Year: 2024
Title: Activation of automethylated PRC2 by dimerization on chromatin.
Authors: Paul V Sauer / Egor Pavlenko / Trinity Cookis / Linda C Zirden / Juliane Renn / Ankush Singhal / Pascal Hunold / Michaela N Hoehne-Wiechmann / Olivia van Ray / Farnusch Kaschani / Markus ...Authors: Paul V Sauer / Egor Pavlenko / Trinity Cookis / Linda C Zirden / Juliane Renn / Ankush Singhal / Pascal Hunold / Michaela N Hoehne-Wiechmann / Olivia van Ray / Farnusch Kaschani / Markus Kaiser / Robert Hänsel-Hertsch / Karissa Y Sanbonmatsu / Eva Nogales / Simon Poepsel /
Abstract: Polycomb repressive complex 2 (PRC2) is an epigenetic regulator that trimethylates lysine 27 of histone 3 (H3K27me3) and is essential for embryonic development and cellular differentiation. H3K27me3 ...Polycomb repressive complex 2 (PRC2) is an epigenetic regulator that trimethylates lysine 27 of histone 3 (H3K27me3) and is essential for embryonic development and cellular differentiation. H3K27me3 is associated with transcriptionally repressed chromatin and is established when PRC2 is allosterically activated upon methyl-lysine binding by the regulatory subunit EED. Automethylation of the catalytic subunit enhancer of zeste homolog 2 (EZH2) stimulates its activity by an unknown mechanism. Here, we show that human PRC2 forms a dimer on chromatin in which an inactive, automethylated PRC2 protomer is the allosteric activator of a second PRC2 that is poised to methylate H3 of a substrate nucleosome. Functional assays support our model of allosteric trans-autoactivation via EED, suggesting a previously unknown mechanism mediating context-dependent activation of PRC2. Our work showcases the molecular mechanism of auto-modification-coupled dimerization in the regulation of chromatin-modifying complexes.
History
DepositionJun 28, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41146.png

Downloads & links

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Map

FileDownload / File: emd_41146.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPRC-J119-450 monomer bound to H1-nucleosome, non-uniform refinement
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.24401125 - 0.7348247
Average (Standard dev.)0.0017221955 (±0.029898908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41146_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PRC2-J119-450 monomer bound to H1-nucleosome

EntireName: PRC2-J119-450 monomer bound to H1-nucleosome
Components
  • Complex: PRC2-J119-450 monomer bound to H1-nucleosome
    • Complex: Nucleosome
      • Protein or peptide: Histone H1.0
      • DNA: DNA (226-MER)
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone-binding protein RBBP4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
      • DNA: DNA (226-MER)
    • Complex: PRC2
      • Protein or peptide: Protein Jumonji
      • Protein or peptide: Polycomb protein SUZ12
      • Protein or peptide: Histone-lysine N-methyltransferase EZH2
      • Protein or peptide: Polycomb protein EED
      • Protein or peptide: Zinc finger protein AEBP2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: PRC2-J119-450 monomer bound to H1-nucleosome

SupramoleculeName: PRC2-J119-450 monomer bound to H1-nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 290 KDa

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Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #6-#12
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: PRC2

SupramoleculeName: PRC2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5, #9, #13
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H1.0

MacromoleculeName: Histone H1.0 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.209459 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMTENSTS APAAKPKRAK ASKKSTDHPK YSDMIVAAIQ AEKNRAGSSR QSIQKYIKSH YKVGENADSQ IKLSIKRLVT TGVLKQTKG VGASGSFRLA KSDEPKKSVA FKKTKKEIKK VATPKKASKP KKAASKAPTK KPKATPVKKA KKKLAATPKK A KKPKTVKA ...String:
GSHMTENSTS APAAKPKRAK ASKKSTDHPK YSDMIVAAIQ AEKNRAGSSR QSIQKYIKSH YKVGENADSQ IKLSIKRLVT TGVLKQTKG VGASGSFRLA KSDEPKKSVA FKKTKKEIKK VATPKKASKP KKAASKAPTK KPKATPVKKA KKKLAATPKK A KKPKTVKA KPVKASKPKK AKPVKPKAKS SAKRAGKKK

UniProtKB: Histone H1.0

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Macromolecule #2: Protein Jumonji

MacromoleculeName: Protein Jumonji / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.251715 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVQSQPNSPS TTPVKIVEPL LPPPATQISD LSKRKPKTED FLTFLCLRGS PALPNSMVYF GSSQDEEEVE EEDDETEDVK TATNNASSS CQSTPRKGKT HKHVHNGHVF NGSSRSTREK EPVQKHKSKE ATPAKEKHSD HRADSRREQA SANHPAAAPS T GSSAKGLA ...String:
MVQSQPNSPS TTPVKIVEPL LPPPATQISD LSKRKPKTED FLTFLCLRGS PALPNSMVYF GSSQDEEEVE EEDDETEDVK TATNNASSS CQSTPRKGKT HKHVHNGHVF NGSSRSTREK EPVQKHKSKE ATPAKEKHSD HRADSRREQA SANHPAAAPS T GSSAKGLA ATHHHPPLHR SAQDLRKQVS KVNGVTRMSS LGAGVTSAKK MREVRPSPSK TVKYTATVTK GAVTYTKAKR EL VKDTKPN HHKPSSAVNH TISGKTESSN AKTRKQVLSL GGASKSTGPA VNGLKVSGRL NPKSCTKEVG GRQLREGLQL REG LRNSKR RLEEAHQA

UniProtKB: Protein Jumonji

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Macromolecule #3: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.266359 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVLPVKKPKM EHVQADHELF LQAFEKPTQI YRFLRTRNLI APIFLHRTLT YMSHRNSRTN IKRKTFKVDD MLSKVEKMKG EQESHSLSA HLQLTFTGFF HKNDKPSPNS ENEQNSVTLE VLLVKVCHKK RKDVSCPIRQ VPTGKKQVPL NPDLNQTKPG N FPSLAVSS ...String:
MVLPVKKPKM EHVQADHELF LQAFEKPTQI YRFLRTRNLI APIFLHRTLT YMSHRNSRTN IKRKTFKVDD MLSKVEKMKG EQESHSLSA HLQLTFTGFF HKNDKPSPNS ENEQNSVTLE VLLVKVCHKK RKDVSCPIRQ VPTGKKQVPL NPDLNQTKPG N FPSLAVSS NEFEPSNSHM VKSYSLLFRV TRPGRREFNG MINGETNENI DVNEELPARR KRNREDGEKT FVAQMTVFDK NR RLQLLDG EYEVAMQEME ECPISKKRAT WETILDGKRL PPFETFSQGP TLQFTLRWTG ETNDKSTAPI AKPLATRNSE SLH QENKPG SVKPTQTIAV KESLTTDLQT RKEKDTPNEN RQKLRIFYQF LYNNNTRQQT EARDDLHCPW CTLNCRKLYS LLKH LKLCH SRFIFNYVYH PKGARIDVSI NECYDGSYAG NPQDIHRQPG FAFSRNGPVK RTPITHILVC RPKRTKASMS EFLES EDGE VEQQRTYSSG HNRLYFHSDT CLPLRPQEME VDSEDEKDPE WLREKTITQI EEFSDVNEGE KEVMKLWNLH VMKHGF IAD NQMNHACMLF VENYGQKIIK KNLCRNFMLH LVSMHDFNLI SIMSIDKAVT KLREMQ

UniProtKB: Polycomb protein SUZ12

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Macromolecule #4: Histone-lysine N-methyltransferase EZH2

MacromoleculeName: Histone-lysine N-methyltransferase EZH2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine27 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.174984 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAGQTGKKS EKGPVACRKR VKSEYMRLRQ LKRFRRADEV KSMFSSNRQK ILERTEILNQ EWKQRRIQPV HILTSVSSLR GTRECSVTS DLDFPTQVIP LKTLNAVASV PIMYSWSPLQ QNFMVEDETV LHNIPYMGDE VLDQDGTFIE ELIKNYDGKV H GDRECGFI ...String:
SNAGQTGKKS EKGPVACRKR VKSEYMRLRQ LKRFRRADEV KSMFSSNRQK ILERTEILNQ EWKQRRIQPV HILTSVSSLR GTRECSVTS DLDFPTQVIP LKTLNAVASV PIMYSWSPLQ QNFMVEDETV LHNIPYMGDE VLDQDGTFIE ELIKNYDGKV H GDRECGFI NDEIFVELVN ALGQYNDDDD DDDGDDPEER EEKQKDLEDH RDDKESRPPR KFPSDKIFEA ISSMFPDKGT AE ELKEKYK ELTEQQLPGA LPPECTPNID GPNAKSVQRE QSLHSFHTLF CRRCFKYDCF LHRKCNYSFH ATPNTYKRKN TET ALDNKP CGPQCYQHLE GAKEFAAALT AERIKTPPKR PGGRRRGRLP NNSSRPSTPT INVLESKDTD SDREAGTETG GENN DKEEE EKKDETSSSS EANSRCQTPI KMKPNIEPPE NVEWSGAEAS MFRVLIGTYY DNFCAIARLI GTKTCRQVYE FRVKE SSII APAPAEDVDT PPRKKKRKHR LWAAHCRKIQ LKKDGSSNHV YNYQPCDHPR QPCDSSCPCV IAQNFCEKFC QCSSEC QNR FPGCRCKAQC NTKQCPCYLA VRECDPDLCL TCGAADHWDS KNVSCKNCSI QRGSKKHLLL APSDVAGWGI FIKDPVQ KN EFISEYCGEI ISQDEADRRG KVYDKYMCSF LFNLNNDFVV DATRKGNKIR FANHSVNPNC YAKVMMVNGD HRIGIFAK R AIQTGEELFF DYRYSQADAL KYVGIEREME IP

UniProtKB: Histone-lysine N-methyltransferase EZH2

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Macromolecule #5: Polycomb protein EED

MacromoleculeName: Polycomb protein EED / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.267691 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS ...String:
MSEREVSTAP AGTDMPAAKK QKLSSDENSN PDLSGDENDD AVSIESGTNT ERPDTPTNTP NAPGRKSWGK GKWKSKKCKY SFKCVNSLK EDHNQPLFGV QFNWHSKEGD PLVFATVGSN RVTLYECHSQ GEIRLLQSYV DADADENFYT CAWTYDSNTS H PLLAVAGS RGIIRIINPI TMQCIKHYVG HGNAINELKF HPRDPNLLLS VSKDHALRLW NIQTDTLVAI FGGVEGHRDE VL SADYDLL GEKIMSCGMD HSLKLWRINS KRMMNAIKES YDYNPNKTNR PFISQKIHFP DFSTRDIHRN YVDCVRWLGD LIL SKSCEN AIVCWKPGKM EDDIDKIKPS ESNVTILGRF DYSQCDIWYM RFSMDFWQKM LALGNQVGKL YVWDLEVEDP HKAK CTTLT HHKCGAAIRQ TSFSRDSSIL IAVCDDASIW RWDRLR

UniProtKB: Polycomb protein EED

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Macromolecule #7: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #8: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.625634 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGGSSG

UniProtKB: Histone H4

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Macromolecule #9: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String:
MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS

UniProtKB: Histone-binding protein RBBP4

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Macromolecule #10: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.355659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAMSGRGKQ GGKTRAKAKT RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AVRNDEELNK LLGRVTIAQG GVLPNIQSVL LPKCTESSKS AKSK

UniProtKB: Histone H2A type 1

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Macromolecule #11: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #13: Zinc finger protein AEBP2

MacromoleculeName: Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.183195 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAYTRRYSS ISSTIMDVDS TISSGRSTPA MMNGQGSTTS SSKNIAYNCC WDQCQACFNS SPDLADHIRS IHVDGQRGGV FVCLWKGCK VYNTPSTSQS WLQRHMLTHS GDKPFKCVVG GCNASFASQG GLARHVPTHF SQQNSSKVSS QPKAKEESPS K AGMNKRRK ...String:
SNAYTRRYSS ISSTIMDVDS TISSGRSTPA MMNGQGSTTS SSKNIAYNCC WDQCQACFNS SPDLADHIRS IHVDGQRGGV FVCLWKGCK VYNTPSTSQS WLQRHMLTHS GDKPFKCVVG GCNASFASQG GLARHVPTHF SQQNSSKVSS QPKAKEESPS K AGMNKRRK LKNKRRRSLP RPHDFFDAQT LDAIRHRAIC FNLSAHIESL GKGHSVVFHS TVIAKRKEDS GKIKLLLHWM PE DILPDVW VNESERHQLK TKVVHLSKLP KDTALLLDPN IYRTMPQKRL KRTLIRKVFN LYLSKQ

UniProtKB: Zinc finger protein AEBP2

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Macromolecule #6: DNA (226-MER)

MacromoleculeName: DNA (226-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 66.53932 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DG)(DA)(DG)(DC)(DT) (DC)(DC)(DG)(DA)(DC)(DC)(DG)(DA)(DA)(DT) (DG)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DG)(DC)(DA)(DT)(DA)(DC)(DA)(DG)(DG)(DA) (DT) (DG)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DC)(DG)(DG)(DG)(DA)(DG)(DC)(DT) (DC)(DC)(DG)(DA)(DC)(DC)(DG)(DA)(DA)(DT) (DG)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DG)(DC)(DA)(DT)(DA)(DC)(DA)(DG)(DG)(DA) (DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG) (DC)(DC) (DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA) (DC)(DC)(DC) (DC)(DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC) (DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC) (DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG) (DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DC) (DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DG)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA) (DT)(DC)(DC)(DC)(DC)(DC)(DA)(DG) (DC) (DC)(DG)(DC)(DC)(DG)(DG)(DC)(DA)(DG)(DC) (DG)(DC)(DA)(DG)(DC)(DG)(DC)(DC)(DT) (DG)(DA)(DC)(DG)(DG)(DG)(DC)(DA)(DC)(DA) (DC)(DA)(DG)(DT)(DC)

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Macromolecule #12: DNA (226-MER)

MacromoleculeName: DNA (226-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 65.905852 KDa
SequenceString: (DG)(DA)(DC)(DT)(DG)(DT)(DG)(DT)(DG)(DC) (DC)(DC)(DG)(DT)(DC)(DA)(DG)(DA)(DC)(DG) (DC)(DT)(DG)(DC)(DG)(DC)(DC)(DG)(DC) (DC)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DG) (DA) (DG)(DA)(DA)(DT)(DC)(DC) ...String:
(DG)(DA)(DC)(DT)(DG)(DT)(DG)(DT)(DG)(DC) (DC)(DC)(DG)(DT)(DC)(DA)(DG)(DA)(DC)(DG) (DC)(DT)(DG)(DC)(DG)(DC)(DC)(DG)(DC) (DC)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DG) (DA) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG) (DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG) (DC)(DC)(DC)(DT)(DA)(DT)(DT) (DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA)(DG)(DC) (DC)(DC)(DC)(DA)(DG)(DC) (DA)(DC)(DC)(DG)(DC)(DC)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA) (DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DC)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT) (DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA)(DT)(DT) (DA)(DC)(DC) (DC)(DC)(DC)(DC)(DA)(DG)(DT)(DC)(DC)(DC) (DC)(DA)(DG)(DG)(DC)(DA)(DC) (DG)(DT) (DG)(DC)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC)(DC)(DC) (DG) (DT)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DC)(DA) (DC)(DA)(DT)(DC)(DA)(DT)(DT)(DC)(DG) (DA)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DT)(DC) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #14: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 14 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

7334

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55918
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8tb9:
PRC2-J119-450 monomer bound to H1-nucleosome

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