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- EMDB-11912: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome. -

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Open data

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Basic information

Entry

Database: EMDB / ID: EMD-11912

Title

Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome.

Map data

Shows the Relion 3.0 postprocessed (b-factor = -90.7) cryo-EM map of the overall PHF1-PRC2:di-Nuc structure.

Sample

Complex: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome
- Complex: Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Polycomb protein SUZ12
  - Protein or peptide: x 3 types
- Complex: Histones
  - Protein or peptide: x 16 types
- Complex: Widom601 DNA + linker
  - RNA: x 2 types

Function / homology

Function and homology information

negative regulation of epidermal cell differentiation / : / : / transcription corepressor binding => GO:0001222 / subtelomeric heterochromatin formation => GO:0031509 / : / : / : / regulation of kidney development / hepatocyte homeostasis ...negative regulation of epidermal cell differentiation / : / : / transcription corepressor binding => GO:0001222 / subtelomeric heterochromatin formation => GO:0031509 / : / : / : / regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / random inactivation of X chromosome / primary miRNA binding / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / facultative heterochromatin formation / histone H3K27 methyltransferase activity / positive regulation of cell cycle G1/S phase transition / chromatin => GO:0000785 / negative regulation of G0 to G1 transition / chromatin silencing complex / ESC/E(Z) complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / RSC-type complex / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / negative regulation of cell differentiation / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / ribonucleoprotein complex binding / heterochromatin formation / positive regulation of epithelial to mesenchymal transition / keratinocyte differentiation / protein localization to chromatin / enzyme activator activity / methylated histone binding / SUMOylation of chromatin organization proteins / B cell differentiation / transcription corepressor binding / positive regulation of GTPase activity / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / stem cell differentiation / liver regeneration / hippocampus development / promoter-specific chromatin binding / positive regulation of MAP kinase activity / protein modification process / positive regulation of protein serine/threonine kinase activity / regulation of circadian rhythm / negative regulation of DNA-binding transcription factor activity / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / HCMV Early Events / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / nucleosome / rhythmic process / nucleosome assembly / response to estradiol / chromatin organization / methylation / Oxidative Stress Induced Senescence / cell population proliferation / chromosome, telomeric region / nuclear body / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / synapse / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Homo sapiens (human) /

Xenopus laevis (African clawed frog) / synthetic construct (others)

Method

single particle reconstruction / cryo EM / Resolution: 5.24 Å

Authors

Finogenova K / Benda C / Poepsel S / Schaefer IB / Strauss M / Mueller J

Funding support

Germany, 2 items

Citation

Journal: Elife / Year: 2020
Title: Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3.
Authors: Ksenia Finogenova / Jacques Bonnet / Simon Poepsel / Ingmar B Schäfer / Katja Finkl / Katharina Schmid / Claudia Litz / Mike Strauss / Christian Benda / Jürg Müller /

Abstract: Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 ...

History

Deposition	Oct 29, 2020	-
Header (metadata) release	Dec 9, 2020	-
Map release	Dec 9, 2020	-
Update	Dec 9, 2020	-
Current status	Dec 9, 2020	Processing site: PDBe / Status: Released

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Structure visualization

Movie	Surface view with section colored by density value Surface level: 0.0263 Imaged by UCSF Chimera Download Surface view colored by cylindrical radius Surface level: 0.0263 Imaged by UCSF Chimera Download Movie viewer
Structure viewer	EM map: SurfViewMolmilJmol/JSmol
Supplemental images	emd_11912.png

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Downloads & links

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EMDB archive

Map data	emd_11912.map.gz	6.7 MB		EMDB map data format
Header (meta data)	emd-11912-v30.xml emd-11912.xml	32.5 KB 32.5 KB	Display Display	EMDB header
Images	emd_11912.png	95.1 KB
Archive directory	http://ftp.pdbj.org/pub/emdb/structures/EMD-11912 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11912	HTTPS FTP

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Validation report

Summary document	emd_11912_validation.pdf.gz	203.5 KB	Display	EMDB validaton report
Full document	emd_11912_full_validation.pdf.gz	202.6 KB	Display
Data in XML	emd_11912_validation.xml.gz	6.4 KB	Display
Arichive directory	https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11912 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11912	HTTPS FTP

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Related structure data

Related structure data	11910C 7at8C C: citing same article (ref.)
Similar structure data	7306 6qfb-d 5y2z-d 7308 3605 11237 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

EMDB pages	EMDB (EBI/PDBe) / EMDataResource
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (22) #177 - Sep 2014 Apoptosomes similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #245 - May 2020 Spliceosomes similarity (2) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (2) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (21) #172 - Apr 2014 RecA and Rad51 similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (2) #122 - Feb 2010 Enhanceosome similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

EMDB pages

EMDB (EBI/PDBe) /

EMDataResource

Related items in Molecule of the Month

#7 - Jul 2000
Nucleosome
similarity (22)
#177 - Sep 2014
Apoptosomes
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#245 - May 2020
Spliceosomes
similarity (2)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (2)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (21)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (2)
#122 - Feb 2010
Enhanceosome
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)

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Map

File

Download / File: emd_11912.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)

Annotation

Shows the Relion 3.0 postprocessed (b-factor = -90.7) cryo-EM map of the overall PHF1-PRC2:di-Nuc structure.

Voxel size

X=Y=Z: 1.746 Å

Density

Contour Level	By AUTHOR: 0.0263 / Movie #1: 0.0263
Minimum - Maximum	-0.050269138 - 0.12714648
Average (Standard dev.)	0.00018827384 (±0.0025756985)

Symmetry

Space group: 1

Details

EMDB XML:

Map geometry

Axis order	X	Y	Z
Origin	0	0	0
Dimensions	312	312	312
Spacing	312	312	312

Cell

A=B=C: 544.752 Å
α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.746	1.746	1.746
M x/y/z	312	312	312
origin x/y/z	0.000	0.000	0.000
length x/y/z	544.752	544.752	544.752
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	240	240	240
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	312	312	312
D min/max/mean	-0.050	0.127	0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome

Entire	Name: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome
Components	Complex: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome Complex: Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Polycomb protein SUZ12 Protein or peptide: Histone-lysine N-methyltransferase EZH2 Protein or peptide: Polycomb protein EED Protein or peptide: Polycomb protein SUZ12 Complex: Histones Protein or peptide: Histone H3.2 Protein or peptide: Histone H4 Protein or peptide: Histone H2A Protein or peptide: Histone H2B Protein or peptide: Histone H3.2 Protein or peptide: Histone H4 Protein or peptide: Histone H2A Protein or peptide: Histone H2B Protein or peptide: Histone H3.2 Protein or peptide: Histone H4 Protein or peptide: Histone H2A Protein or peptide: Histone H2B Protein or peptide: Histone H3.2 Protein or peptide: Histone H4 Protein or peptide: Histone H2A Protein or peptide: Histone H2B Complex: Widom601 DNA + linker RNA: Widom601 DNA + linker RNA: Widom601 DNA + linker

Entire

Name: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome

Components

Complex: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome
- Complex: Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Polycomb protein SUZ12
  - Protein or peptide: Histone-lysine N-methyltransferase EZH2
  - Protein or peptide: Polycomb protein EED
  - Protein or peptide: Polycomb protein SUZ12
- Complex: Histones
  - Protein or peptide: Histone H3.2
  - Protein or peptide: Histone H4
  - Protein or peptide: Histone H2A
  - Protein or peptide: Histone H2B
  - Protein or peptide: Histone H3.2
  - Protein or peptide: Histone H4
  - Protein or peptide: Histone H2A
  - Protein or peptide: Histone H2B
  - Protein or peptide: Histone H3.2
  - Protein or peptide: Histone H4
  - Protein or peptide: Histone H2A
  - Protein or peptide: Histone H2B
  - Protein or peptide: Histone H3.2
  - Protein or peptide: Histone H4
  - Protein or peptide: Histone H2A
  - Protein or peptide: Histone H2B
- Complex: Widom601 DNA + linker
  - RNA: Widom601 DNA + linker
  - RNA: Widom601 DNA + linker

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Supramolecule #1: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome

Supramolecule	Name: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Density for the bottom lobe of PRC2 comprising the N-term of SUZ12 and RBBP4 or PHF1 could not be observed in the map.

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Supramolecule #2: Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Po...

Supramolecule	Name: Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Polycomb protein SUZ12 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)	Organism: Homo sapiens (human)
Recombinant expression	Organism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: Histones

Supramolecule	Name: Histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#19
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)

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Supramolecule #4: Widom601 DNA + linker

Supramolecule	Name: Widom601 DNA + linker / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #20-#21
Source (natural)	Organism: synthetic construct (others)

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Macromolecule #1: Histone-lysine N-methyltransferase EZH2

Macromolecule	Name: Histone-lysine N-methyltransferase EZH2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)	Organism: Homo sapiens (human)
Recombinant expression	Organism: Trichoplusia ni (cabbage looper)
Sequence	String: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVH ILTSVSSLRG TRECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN F MVEDETVL HNIPYMGDEV LDQDGTFIEE LIKNYDGKVH GDRECGFIND ...String: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVH ILTSVSSLRG TRECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN F MVEDETVL HNIPYMGDEV LDQDGTFIEE LIKNYDGKVH GDRECGFIND EIFVELVNAL GQ YNDDDDD DDGDDPEERE EKQKDLEDHR DDKESRPPRK FPSDKIFEAI SSMFPDKGTA EEL KEKYKE LTEQQLPGAL PPECTPNIDG PNAKSVQREQ SLHSFHTLFC RRCFKYDCFL HRKC NYSFH ATPNTYKRKN TETALDNKPC GPQCYQHLEG AKEFAAALTA ERIKTPPKRP GGRRR GRLP NNSSRPSTPT INVLESKDTD SDREAGTETG GENNDKEEEE KKDETSSSSE ANSRCQ TPI KMKPNIEPPE NVEWSGAEAS MFRVLIGTYY DNFCAIARLI GTKTCRQVYE FRVKESS II APAPAEDVDT PPRKKKRKHR LWAAHCRKIQ LKKDGSSNHV YNYQPCDHPR QPCDSSCP C VIAQNFCEKF CQCSSECQNR FPGCRCKAQC NTKQCPCYLA VRECDPDLCL TCGAADHWD SKNVSCKNCS IQRGSKKHLL LAPSDVAGWG IFIKDPVQKN EFISEYCGEI ISQDEADRRG KVYDKYMCS FLFNLNNDFV VDATRKGNKI RFANHSVNPN CYAKVMMVNG DHRIGIFAKR A IQTGEELF FDYRYSQADA LKYVGIEREM EIP

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Macromolecule #2: Polycomb protein EED

Macromolecule	Name: Polycomb protein EED / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)	Organism: Homo sapiens (human)
Recombinant expression	Organism: Trichoplusia ni (cabbage looper)
Sequence	String: 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 SKSGRAILHS HQQCMRDPVS PNLRQHLSCE NAIVCWKPGK MEDDIDKIKP SESNVTILGR FDYSQCDIWY MRFSMDFWQK MLALGNQVGK LYVWDLEVED PHKAKCTTLT HHKCGAAIRQ TSFSRDSSIL IAVCDDASIW RWDRLR

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Macromolecule #3: Polycomb protein SUZ12

Macromolecule	Name: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)	Organism: Homo sapiens (human)
Recombinant expression	Organism: Trichoplusia ni (cabbage looper)
Sequence	String: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQAF EKPTQIYRFL RTRNLIAPIF LHRTLTYMSH RNSRTNIKRK TFKVDDMLSK VEKMKGEQES HSLSAHLQLT FTGFFHKNDK ...String: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQAF EKPTQIYRFL RTRNLIAPIF LHRTLTYMSH RNSRTNIKRK TFKVDDMLSK VEKMKGEQES HSLSAHLQLT FTGFFHKNDK PSPNSENEQN SVTLEVLLVK VCHKKRKDVS CPIRQVPTGK KQVPLNPDLN QTKPGNFPSL AVSSNEFEPS NSHMVKSYSL LFRVTRPGRR EFNGMINGET NENIDVNEEL PARRKRNRED GEKTFVAQMT VFDKNRRLQL LDGEYEVAMQ EMEECPISKK RATWETILDG KRLPPFETFS QGPTLQFTLR WTGETNDKST APIAKPLATR NSESLHQENK PGSVKPTQTI AVKESLTTDL QTRKEKDTPN ENRQKLRIFY QFLYNNNTRQ QTEARDDLHC PWCTLNCRKL YSLLKHLKLC HSRFIFNYVY HPKGARIDVS INECYDGSYA GNPQDIHRQP GFAFSRNGPV KRTPITHILV CRPKRTKASM SEFLESEDGE VEQQRTYSSG HNRLYFHSDT CLPLRPQEME VDSEDEKDPE WLREKTITQI EEFSDVNEGE KEVMKLWNLH VMKHGFIADN QMNHACMLFV ENYGQKIIKK NLCRNFMLHL VSMHDFNLIS IMSIDKAVTK LREMQQKLEK GESASPANEE ITEEQNGTAN GFSEINSKEK ALETDSVSGV SKQSKKQKL

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Macromolecule #4: Histone H3.2

Macromolecule	Name: Histone H3.2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA

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Macromolecule #5: Histone H4

Macromolecule	Name: Histone H4 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

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Macromolecule #6: Histone H2A

Macromolecule	Name: Histone H2A / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK

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Macromolecule #7: Histone H2B

Macromolecule	Name: Histone H2B / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK

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Macromolecule #8: Histone H3.2

Macromolecule	Name: Histone H3.2 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA

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Macromolecule #9: Histone H4

Macromolecule	Name: Histone H4 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

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Macromolecule #10: Histone H2A

Macromolecule	Name: Histone H2A / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK

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Macromolecule #11: Histone H2B

Macromolecule	Name: Histone H2B / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK

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Macromolecule #12: Histone H3.2

Macromolecule	Name: Histone H3.2 / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA

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Macromolecule #13: Histone H4

Macromolecule	Name: Histone H4 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

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Macromolecule #14: Histone H2A

Macromolecule	Name: Histone H2A / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK

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Macromolecule #15: Histone H2B

Macromolecule	Name: Histone H2B / type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK

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Macromolecule #16: Histone H3.2

Macromolecule	Name: Histone H3.2 / type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA

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Macromolecule #17: Histone H4

Macromolecule	Name: Histone H4 / type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

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Macromolecule #18: Histone H2A

Macromolecule	Name: Histone H2A / type: protein_or_peptide / ID: 18 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK

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Macromolecule #19: Histone H2B

Macromolecule	Name: Histone H2B / type: protein_or_peptide / ID: 19 / Enantiomer: LEVO
Source (natural)	Organism: Xenopus laevis (African clawed frog)
Recombinant expression	Organism: Escherichia coli (E. coli)
Sequence	String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK

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Macromolecule #20: Widom601 DNA + linker

Macromolecule	Name: Widom601 DNA + linker / type: rna / ID: 20
Source (natural)	Organism: synthetic construct (others)
Sequence	String: ATCAATATCC ACCTGCAGAT TCTACCAAAA GTGTATTTGG AAACTGCTCC ATCAAAAGGC ATGTTCAGCT GAATTCAGC TGAACATGCC TTTTGATGGA GCAGTTTCCA AATACACTTT TGGTAGAATC TGCAGGTGGA T ATTGATAG CGATCTCACG GGGTGATGCT ...String: ATCAATATCC ACCTGCAGAT TCTACCAAAA GTGTATTTGG AAACTGCTCC ATCAAAAGGC ATGTTCAGCT GAATTCAGC TGAACATGCC TTTTGATGGA GCAGTTTCCA AATACACTTT TGGTAGAATC TGCAGGTGGA T ATTGATAG CGATCTCACG GGGTGATGCT CGATACTCAT AATCAAAATA TCCACCTGCA GATTCTACCA AA AGTGTAT TTGGAAACTG CTCCATCAAA AGGCATGTTC AGCTGAATTC AGCTGAACAT GCCTTTTGAT GGA GCAGTT TCCAAATACA CTTTTGGTAG AATCTGCAGG TGGATATTGA TTATGCATGC A

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Macromolecule #21: Widom601 DNA + linker

Macromolecule	Name: Widom601 DNA + linker / type: rna / ID: 21
Source (natural)	Organism: synthetic construct (others)
Sequence	String: TGCATGCATA ATCAATATCC ACCTGCAGAT TCTACCAAAA GTGTATTTGG AAACTGCTCC ATCAAAAGGC ATGTTCAGC TGAATTCAGC TGAACATGCC TTTTGATGGA GCAGTTTCCA AATACACTTT TGGTAGAATC T GCAGGTGG ATATTTTGAT TATGAGTATC ...String: TGCATGCATA ATCAATATCC ACCTGCAGAT TCTACCAAAA GTGTATTTGG AAACTGCTCC ATCAAAAGGC ATGTTCAGC TGAATTCAGC TGAACATGCC TTTTGATGGA GCAGTTTCCA AATACACTTT TGGTAGAATC T GCAGGTGG ATATTTTGAT TATGAGTATC GAGCATCACC CCGTGAGATC GCTATCAATA TCCACCTGCA GA TTCTACC AAAAGTGTAT TTGGAAACTG CTCCATCAAA AGGCATGTTC AGCTGAATTC AGCTGAACAT GCC TTTTGA TGGAGCAGTT TCCAAATACA CTTTTGGTAG AATCTGCAGG TGGATATTGA T

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Experimental details

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Structure determination

Method	cryo EM
Processing	single particle reconstruction
Aggregation state	particle

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Sample preparation

Buffer	pH: 7.8
Vitrification	Cryogen name: ETHANE-PROPANE

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Electron microscopy

Microscope	FEI TITAN KRIOS
Image recording	Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.96 e/Å²
Electron beam	Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics	Illumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup model	Type of model: PDB ENTRY PDB model - PDB ID: 5hyn Details: Other PDBs: 6T9L and 1AOI. Also model of PRC2-AEBP2 on dinucleosome in Supplementary dataset 1 in Poepsel et al. (2018) including crystal structures of nucleosomes, PDB 3LZ1.
Final reconstruction	Resolution.type: BY AUTHOR / Resolution: 5.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45849
Initial angle assignment	Type: MAXIMUM LIKELIHOOD
Final angle assignment	Type: MAXIMUM LIKELIHOOD

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+Entire : Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome

+Supramolecule #1: Cryo-EM map of PHF1-PRC2 on a heterodimeric dinucleosome

+Supramolecule #2: Histone-lysine N-methyltransferase EZH2, Polycomb protein EED, Po...

+Supramolecule #3: Histones

+Supramolecule #4: Widom601 DNA + linker

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

+Macromolecule #2: Polycomb protein EED

+Macromolecule #3: Polycomb protein SUZ12

+Macromolecule #4: Histone H3.2

+Macromolecule #5: Histone H4

+Macromolecule #6: Histone H2A

+Macromolecule #7: Histone H2B

+Macromolecule #8: Histone H3.2

+Macromolecule #9: Histone H4

+Macromolecule #10: Histone H2A

+Macromolecule #11: Histone H2B

+Macromolecule #12: Histone H3.2

+Macromolecule #13: Histone H4

+Macromolecule #14: Histone H2A

+Macromolecule #15: Histone H2B

+Macromolecule #16: Histone H3.2

+Macromolecule #17: Histone H4

+Macromolecule #18: Histone H2A

+Macromolecule #19: Histone H2B

+Macromolecule #20: Widom601 DNA + linker

+Macromolecule #21: Widom601 DNA + linker

-Experimental details

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