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- EMDB-23103: PRC2:EZH1 dimer bound to a nucleosome (composite map) -

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Basic information

Entry
Database: EMDB / ID: EMD-23103
TitlePRC2:EZH1 dimer bound to a nucleosome (composite map)
Map dataPRC2:EZH1 dimer-nucleosome (composite map)
Sample
  • Complex: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
    • Protein or peptide: x 4 types
  • Protein or peptide: x 6 types
  • DNA: x 1 types
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / histone H3K27 methyltransferase activity / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification ...[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / histone H3K27 methyltransferase activity / facultative heterochromatin formation / NURF complex / NuRD complex / regulation of cell fate specification / 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 / regulation of stem cell differentiation / chromatin silencing complex / RSC-type complex / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / lncRNA binding / spinal cord development / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / ATPase complex / histone methyltransferase activity / Sin3-type complex / Transcriptional Regulation by E2F6 / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of cell differentiation / G0 and Early G1 / nucleosome binding / subtelomeric heterochromatin formation / anatomical structure morphogenesis / heterochromatin / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / enzyme activator activity / methylated histone binding / SUMOylation of chromatin organization proteins / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / hippocampus development / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / promoter-specific chromatin binding / molecular condensate scaffold activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / heterochromatin formation / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / nucleosome assembly / chromosome / histone binding / Oxidative Stress Induced Senescence / methylation / Potential therapeutics for SARS / DNA replication / cell population proliferation / chromosome, telomeric region / nuclear body / chromatin remodeling / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
EZH1, 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 ...EZH1, 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 / : / 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 / SANT/Myb domain / Zinc finger C2H2 type domain signature. / G-protein beta WD-40 repeat / 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 / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Polycomb protein EED / Histone-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH1
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsGrau DJ / Armache KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115882 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction.
Authors: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas ...Authors: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas Walz / Karim-Jean Armache /
Abstract: Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the ...Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.
History
DepositionDec 12, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23103.png

Downloads & links

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Map

FileDownload / File: emd_23103.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPRC2:EZH1 dimer-nucleosome (composite map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.01
Minimum - Maximum-0.041071013 - 0.073443495
Average (Standard dev.)-0.0003315232 (±0.0018965694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z405.000405.000405.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0410.073-0.000

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Supplemental data

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Sample components

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Entire : PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome

EntireName: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
Components
  • Complex: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
  • Protein or peptide: EZH1
  • Protein or peptide: EED
  • Protein or peptide: SUZ12
  • Protein or peptide: RBAP48
  • Protein or peptide: AEBP2
  • Protein or peptide: JARID2
  • DNA: 167bp DNA 601 strand

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Supramolecule #1: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome

SupramoleculeName: PRC2:EZH1_A from a PRC2:EZH1 dimer bound to a nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 266 KDa

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVALFED TNLCAIHAK RVTIMPKDIQ LARRIRGERA

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE TRGVLKVFLE NVIRDAVTYT EHAKRKTVTA MDVVYALKRQ GRTLYGFGG

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KAKTRSSRAG LQFPVGRVHR LLRKGNYAER VGAGAPVYLA AVLEYLTAEI LELAGNAARD NKKTRIIPRH LQLAVRNDE ELNKLLGRVT IAQGGVLPNI QSVLLP

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKH AVSEGTKAVT KYTSAK

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Macromolecule #6: EZH1

MacromoleculeName: EZH1 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: meipnpptsk citywkrkv k seymrlrq lk rlqanmg aka lyvanf akvq ektqi lneew kklr vqpvqs mkp vsghpfl kk ctiesifp g fasqhmlmr slntvalvpi myswsplqq n fmvedetv lc nipymgd evk eedetf ieel innyd ...String:
meipnpptsk citywkrkv k seymrlrq lk rlqanmg aka lyvanf akvq ektqi lneew kklr vqpvqs mkp vsghpfl kk ctiesifp g fasqhmlmr slntvalvpi myswsplqq n fmvedetv lc nipymgd evk eedetf ieel innyd gkvhg eeem ipgsvl isd avflelv da lnqysdee e eghndtsdg kqddskedlp vtrkrkrha i egnkkssk kq fpndmif sai asmfpe ngvp ddmke ryrel tems dpnalp pqc tpnidgp na ksvqreqs l hsfhtlfcr rcfkydcflh pfhatpnvy k rknkeiki ep epcgtdc fll legake yaml hnprs kcsgr rrrr hhivsa scs nasasav ae tkegdsdr d tgndwasss seansrcqtp tkqkaspap p qlcvveap se pvewtga ees lfrvfh gtyf nnfcs iarll gtkt ckqvfq fav keslilk lp tdelmnps q kkkrkhrlw aahcrkiqlk kdnsstqvy n yqpcdhpd rp cdstcpc imt qnfcek fcqc npdcq nrfpg crck tqcntk qcp cylavre cd pdlcltcg a sehwdckvv sckncsiqrg lkkhlllap s dvagwgtf ik esvqkne fis eycgel isqd eadrr gkvyd kyms sflfnl nnd fvvdatr kg nkirfanh s vnpncyakv vmvngdhrig ifakraiqa g eelffdyr ys qadalky vgi eretdv l

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Macromolecule #7: EED

MacromoleculeName: EED / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mserevstap agtdmpaak k qklssden sn pdlsgde ndd avsies gtnt erpdt ptntp napg rkswgk gkw kskkcky sf kcvnslke d hnqplfgvq fnwhskegdp lvfatvgsn r vtlyechs qg eirllqs yvd adaden fytc awtyd ...String:
mserevstap agtdmpaak k qklssden sn pdlsgde ndd avsies gtnt erpdt ptntp napg rkswgk gkw kskkcky sf kcvnslke d hnqplfgvq fnwhskegdp lvfatvgsn r vtlyechs qg eirllqs yvd adaden fytc awtyd sntsh plla vagsrg iir iinpitm qc ikhyvghg n ainelkfhp rdpnlllsvs kdhalrlwn i qtdtlvai fg gveghrd evl sadydl lgek imscg mdhsl klwr inskrm mna ikesydy np nktnrpfi s qkihfpdfs trdihrnyvd cvrwlgdli l skscenai vc wkpgkme ddi dkikps esnv tilgr fdysq cdiw ymrfsm dfw qkmlalg nq vgklyvwd l evedphkak cttlthhkcg aairqtsfs r dssiliav cd dasiwrw drl r

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Macromolecule #8: SUZ12

MacromoleculeName: SUZ12 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: mapqkhgggg gggsgpsag s ggggfggs aa vaaatas ggk sgggsc gggg sysas ssssa aaaa gaavlp vkk pkmehvq ad helflqaf e kptqiyrfl rtrnliapif lhrtltyms h rnsrtnik rk tfkvddm lsk vekmkg eqes hslsa ...String:
mapqkhgggg gggsgpsag s ggggfggs aa vaaatas ggk sgggsc gggg sysas ssssa aaaa gaavlp vkk pkmehvq ad helflqaf e kptqiyrfl rtrnliapif lhrtltyms h rnsrtnik rk tfkvddm lsk vekmkg eqes hslsa hlqlt ftgf fhkndk psp nseneqn sv tlevllvk v chkkrkdvs cpirqvptgk kqvplnpdl n qtkpgnfp sl avssnef eps nshmvk sysl lfrvt rpgrr efng minget nen idvneel pa rrkrnred g ektfvaqmt vfdknrrlql ldgeyevam q emeecpis kk ratweti ldg krlppf etfs qgptl qftlr wtge tndkst api akplatr ns eslhqenk p gsvkptqti avkeslttdl qtrkekdtp n enrqklri fy qflynnn trq qteard dlhc pwctl ncrkl ysll khlklc hsr fifnyvy hp kgaridvs i necydgsya gnpqdihrqp gfafsrngp v krtpithi lv crpkrtk asm sefles edge veqqr tyssg hnrl yfhsdt clp lrpqeme vd sedekdpe w lrektitqi eefsdvnege kevmklwnl h vmkhgfia dn qmnhacm lfv enygqk iikk nlcrn fmlhl vsmh dfnlis ims idkavtk lr emqqklek g esaspanee iteeqngtan gfseinske k aletdsvs gv skqskkq kl

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Macromolecule #9: RBAP48

MacromoleculeName: RBAP48 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: madkeaafdd aveervine e ykiwkknt pf lydlvmt hal ewpslt aqwl pdvtr pegkd fsih rlvlgt hts deqnhlv ia svqlpndd a qfdashyds ekgefggfgs vsgkieiei k inhegevn ra rympqnp cii atktps sdvl vfdyt ...String:
madkeaafdd aveervine e ykiwkknt pf lydlvmt hal ewpslt aqwl pdvtr pegkd fsih rlvlgt hts deqnhlv ia svqlpndd a qfdashyds ekgefggfgs vsgkieiei k inhegevn ra rympqnp cii atktps sdvl vfdyt khpsk pdps gecnpd lrl rghqkeg yg lswnpnls g hllsasddh ticlwdisav pkegkvvda k tiftghta vv edvswhl lhe slfgsv addq klmiw dtrsn ntsk pshsvd aht aevncls fn pysefila t gsadktval wdlrnlklkl hsfeshkde i fqvqwsph ne tilassg tdr rlnvwd lski geeqs pedae dgpp ellfih ggh takisdf sw npnepwvi c svsednimq vwqmaeniyn dedpegsvd p egqgs

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Macromolecule #10: AEBP2

MacromoleculeName: AEBP2 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: mssdgeplsr mdsedsiss t imdvdsti ss grstpam mng qgstts sskn iaync cwdqc qacf nsspdl adh irsihvd gq rggvfvcl w kgckvyntp stsqswlqrh mlthsgdkp f kcvvggcn as fasqggl arh vpthfs qqns skvss ...String:
mssdgeplsr mdsedsiss t imdvdsti ss grstpam mng qgstts sskn iaync cwdqc qacf nsspdl adh irsihvd gq rggvfvcl w kgckvyntp stsqswlqrh mlthsgdkp f kcvvggcn as fasqggl arh vpthfs qqns skvss qpkak eesp skagmn krr klknkrr rs lprphdff d aqtldairh raicfnlsah ieslgkghs v vfhstvia kr kedsgki kll lhwmpe dilp dvwvn eserh qlkt kvvhls klp kdtalll dp niyrtmpq k rlkr

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Macromolecule #11: JARID2

MacromoleculeName: JARID2 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: mskerpkrni iqkkyddsd g ipwseerv vr kvlylsl kef knsqkr qhae giags lktvn gllg ndqskg lgp aseqsen ek ddasqvss t sndvsssdf eegpsrkrpr lqaqrkfaq s qpnspstt pv kivepll ppp atqisd lskr kpkte ...String:
mskerpkrni iqkkyddsd g ipwseerv vr kvlylsl kef knsqkr qhae giags lktvn gllg ndqskg lgp aseqsen ek ddasqvss t sndvsssdf eegpsrkrpr lqaqrkfaq s qpnspstt pv kivepll ppp atqisd lskr kpkte dfltf lclr gspalp nsm vyfgssq de eeveeedd e tedvktatn nassscqstp rkgkthkhv h nghvfngs sr strekep vqk hkskea tpak ekhsd hrads rreq asanhp aaa pstgssa kg laathhhp p lhrsaqdlr kqvskvngvt rmsslgagv t sakkmrev rp spsktvk yta tvtkga vtyt kakre lvkdt kpnh hkpssa vnh tisgkte ss naktrkqv l slggaskst gpavnglkvs grlnpksct k evggrqlr eg lqlregl rns krrlee ahqa ekpqs ppkkm kgaa gpaegp gkk apaergl ln ghvkkevp e rslernrpk ratagkstpg rqahgkads a scenrsts qp esvhkpq dsg kaekgg gkag waamd eipvl rpsa kefhdp liy iesvraq ve kfgmcrvi p ppdwrpeck lndemrfvtq iqhihklgr r wgpnvqrl ac ikkhlks qgi tmdelp ligg celdl acffr line mggmqq vtd lkkwnkl ad mlriprta q drlaklqea ycqyllsyds lspeehrrl e kevlmeke il ekrkgpl egh tendhh kfhp lprfe pkngl ihgv aprngf rsk lkevgqa ql ktgrrrlf a qekevvkee eedkgvlndf hkciykgrs v slttfyrt ar nimsmcf ske papaei eqey wrlve ekdch vavh cgkvdt nth gsgfpvg ks epfsrhgw n ltvlpnntg silrhlgavp gvtipwlni g mvfstscw sr dqnhlpy idy lhtgad ciwy cipae eenkl edvv htllqa ngt pglqmle sn vmispevl c kegikvhrt vqqsgqfvvc fpgsfvskv c cgysvset vh fattqwt smg fetake mkrr hiakp fsmek llyq iaqaea kke ngptlst is alldelrd t elrqrrqlf eaglhssary gshdgsstv a dgkkkprk wl qletser rcq icqhlc ylsm vvqen envvf clec alrhve kqk scrglkl my rydeeqii s lvnqicgkv sgkngsienc lskptpkrg p rkratvdv pp srlsass ssk sassss

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Macromolecule #5: 167bp DNA 601 strand

MacromoleculeName: 167bp DNA 601 strand / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
TACCCGGGAT ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTA CGCGCTGTCC CCCGCGTTTT AACCGCCAAG GGGATTACTC CCTAGTCTCC AGGCACGTGT C AGATATAT ACATCCGATA TCCCGGGTA

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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

Concentration0.12 mg/mL
BufferpH: 7.9
Component:
ConcentrationNameFormula
20.0 mMHEPES
50.0 mMsodium chlorideNaCl
1.0 mMmagnesium chlorideMgCl2
1.0 mMdithiothreitol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3410000 / Details: Template based picking
CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF correction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Values provided are for the PRC2B map portion of the 3-component composite map. Other parts of the composite map used: nucleosome: 56616 particles, 3.3 angstroms. PRC2A: 18151 particles, 4.1 angstroms.
Number images used: 26440
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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