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- EMDB-43361: PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged -

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Basic information

Entry
Database: EMDB / ID: EMD-43361
TitlePRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged
Map data
Sample
  • Complex: PRC2_AJ1-450 bound to H3K36me3 modified nucleosome with tail engaged
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: EED
    • Protein or peptide: RBAP48
    • Protein or peptide: Protein Jumonji
    • Protein or peptide: Zinc finger protein AEBP2
    • DNA: DNA (26-mer)
    • Protein or peptide: H3K36me3-modified histone H3
    • DNA: DNA (26-MER)
  • Protein or peptide: Isoform 2 of Histone-lysine N-methyltransferase EZH2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
Keywordscomplex / methyltransferase / histone / epigenetics / GENE REGULATION / GENE REGULATION-DNA complex
Function / homology
Function and homology information


regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / CAF-1 complex / DRM complex / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / primary miRNA binding / histone H3K27 methyltransferase activity / pronucleus / ubiquitin-modified histone reader activity ...regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / CAF-1 complex / DRM complex / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / primary miRNA binding / histone H3K27 methyltransferase activity / pronucleus / ubiquitin-modified histone reader activity / facultative heterochromatin formation / positive regulation of cell cycle G1/S phase transition / sex chromatin / NURF complex / NuRD complex / regulatory ncRNA-mediated heterochromatin formation / regulation of cell fate specification / negative regulation of stem cell population maintenance / regulation of stem cell differentiation / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / DNA replication-dependent chromatin assembly / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / chromatin silencing complex / RSC-type complex / positive regulation of dendrite development / histone H3K9me2/3 reader activity / positive regulation of protein serine/threonine kinase activity / spinal cord development / histone H3 methyltransferase activity / histone methyltransferase activity / synaptic transmission, GABAergic / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / histone deacetylase complex / ATPase complex / positive regulation of stem cell population maintenance / positive regulation of MAP kinase activity / Sin3-type complex / Transcriptional Regulation by E2F6 / histone methyltransferase complex / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / G0 and Early G1 / lncRNA binding / subtelomeric heterochromatin formation / positive regulation of GTPase activity / positive regulation of epithelial to mesenchymal transition / pericentric heterochromatin / ribonucleoprotein complex binding / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / RNA polymerase II core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / B cell differentiation / stem cell differentiation / Chromatin modifying enzymes / heterochromatin / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / negative regulation of cytokine production involved in inflammatory response / nucleosome binding / hippocampus development / negative regulation of cell migration / telomere organization / Interleukin-7 signaling / ChAHP complex assembly / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of transforming growth factor beta receptor signaling pathway / RNA Polymerase I Promoter Opening / Regulation of PTEN gene transcription / transcription corepressor binding / Assembly of the ORC complex at the origin of replication / FXIIa activates plasma kallikrein-kinin system / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / central nervous system development / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / brain development / PRC2 methylates histones and DNA / NuRD complex assembly / Regulation of endogenous retroelements by KRAB-ZFP proteins / Interaction of NuRD complexes with transcription factors / Defective pyroptosis / ubiquitin binding / HDACs deacetylate histones / CHD1 and CHD2 subfamily / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / epigenetic regulation of gene expression / CHD6, CHD7, CHD8, CHD9 subfamily
Similarity search - Function
: / : / AEBP2-like, C-terminal SH3 domain / : / Polycomb protein SUZ12-like, Zn 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 ...: / : / AEBP2-like, C-terminal SH3 domain / : / Polycomb protein SUZ12-like, Zn 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 / : / : / 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 / JmjC domain, hydroxylase / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain / SET domain superfamily / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Polycomb protein EED / Histone H3.1 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCookis T / Nogales E
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127018 United States
National Science Foundation (NSF, United States)GM-08295 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications.
Authors: Trinity Cookis / Alexandria Lydecker / Paul Sauer / Vignesh Kasinath / Eva Nogales /
Abstract: Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is ...Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is regulated by protein cofactors and their crosstalk with histone modifications. Trimethylated histone H3 on K4 (H3K4me3) and K36 (H3K36me3) localize to sites of active transcription and inhibit PRC2 activity through unknown mechanisms. Using cryo-electron microscopy, we reveal that histone H3 tails containing H3K36me3 engage poorly with PRC2 and preclude its effective interaction with chromatin, while H3K4me3 binds to the allosteric site in the EED subunit, acting as an antagonist that competes with activators required for spreading of the H3K27me3 repressive mark. Thus, the location of the H3K4me3 and H3K36me3 modifications along the H3 tail allows them to target two requirements for efficient trimethylation of H3K27 by PRC2. We further show that the JARID2 cofactor modulates PRC2 activity in the presence of these histone modifications.
History
DepositionJan 13, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43361.png

Downloads & links

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Map

FileDownload / File: emd_43361.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å		1.05 Å/pix.
x 384 pix.
= 403.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-0.752412 - 1.6409003
Average (Standard dev.)-0.000021897391 (±0.041402478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43361_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43361_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PRC2_AJ1-450 bound to H3K36me3 modified nucleosome with tail engaged

EntireName: PRC2_AJ1-450 bound to H3K36me3 modified nucleosome with tail engaged
Components
  • Complex: PRC2_AJ1-450 bound to H3K36me3 modified nucleosome with tail engaged
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: EED
    • Protein or peptide: RBAP48
    • Protein or peptide: Protein Jumonji
    • Protein or peptide: Zinc finger protein AEBP2
    • DNA: DNA (26-mer)
    • Protein or peptide: H3K36me3-modified histone H3
    • DNA: DNA (26-MER)
  • Protein or peptide: Isoform 2 of Histone-lysine N-methyltransferase EZH2
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: PRC2_AJ1-450 bound to H3K36me3 modified nucleosome with tail engaged

SupramoleculeName: PRC2_AJ1-450 bound to H3K36me3 modified nucleosome with tail engaged
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.265375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 KESLTTNLQT 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 #2: EED

MacromoleculeName: EED / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.267691 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #3: RBAP48

MacromoleculeName: RBAP48 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #4: Isoform 2 of Histone-lysine N-methyltransferase EZH2

MacromoleculeName: Isoform 2 of 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: 85.492297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVHI LTSVSSLRGT RECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN FMVEDETVLH NIPYMGDEVL DQDGTFIEEL IKNYDGKVHG D RECGFIND ...String:
MGQTGKKSEK GPVCWRKRVK SEYMRLRQLK RFRRADEVKS MFSSNRQKIL ERTEILNQEW KQRRIQPVHI LTSVSSLRGT RECSVTSDL DFPTQVIPLK TLNAVASVPI MYSWSPLQQN FMVEDETVLH NIPYMGDEVL DQDGTFIEEL IKNYDGKVHG D RECGFIND EIFVELVNAL GQYNDDDDDD DGDDPEEREE KQKDLEDHRD DKESRPPRKF PSDKIFEAIS SMFPDKGTAE EL KEKYKEL TEQQLPGALP PECTPNIDGP NAKSVQREQS LHSFHTLFCR RCFKYDCFLH PFHATPNTYK RKNTETALDN KPC GPQCYQ HLEGAKEFAA ALTAERIKTP PKRPGGRRRG RLPNNSSRPS TPTINVLESK DTDSDREAGT ETGGENNDKE EEEK KDETS SSSEANSRCQ TPIKMKPNIE PPENVEWSGA EASMFRVLIG TYYDNFCAIA RLIGTKTCRQ VYEFRVKESS IIAPA PAED VDTPPRKKKR KHRLWAAHCR KIQLKKDGSS NHVYNYQPCD HPRQPCDSSC PCVIAQNFCE KFCQCSSECQ NRFPGC RCK AQCNTKQCPC YLAVRECDPD LCLTCGAADH WDSKNVSCKN CSIQRGSKKH LLLAPSDVAG WGIFIKDPVQ KNEFISE YC GEIISQDEAD RRGKVYDKYM CSFLFNLNND FVVDATRKGN KIRFANHSVN PNCYAKVMMV NGDHRIGIFA KRAIQTGE E LFFDYRYSQA DALKYVGIER EMEIP

UniProtKB: Histone-lysine N-methyltransferase EZH2

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Macromolecule #5: Protein Jumonji

MacromoleculeName: Protein Jumonji / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.174879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SKERPKRNII QKKYDDSDGI PWSEERVVRK VLYLSLKEFK NSQKRQHAEG IAGSLKTVNG LLGNDQSKGL GPASEQSENE KDDASQVSS TSNDVSSSDF EEGPSRKRPR LQAQR(M3L)FAQS QPNSPSTTPV KIVEPLLPPP ATQISDLSKR KPKTEDF LT FLCLRGSPAL ...String:
SKERPKRNII QKKYDDSDGI PWSEERVVRK VLYLSLKEFK NSQKRQHAEG IAGSLKTVNG LLGNDQSKGL GPASEQSENE KDDASQVSS TSNDVSSSDF EEGPSRKRPR LQAQR(M3L)FAQS QPNSPSTTPV KIVEPLLPPP ATQISDLSKR KPKTEDF LT FLCLRGSPAL PNSMVYFGSS QDEEEVEEED DETEDVKTAT NNASSSCQST PRKGKTHKHV HNGHVFNGSS RSTREKEP V QKHKSKEATP AKEKHSDHRA DSRREQASAN HPAAAPSTGS SAKGLAATHH HPPLHRSAQD LRKQVSKVNG VTRMSSLGA GVTSAKKMRE VRPSPSKTVK YTATVTKGAV TYTKAKRELV KDTKPNHHKP SSAVNHTISG KTESSNAKTR KQVLSLGGAS KSTGPAVNG LKVSGRLNPK SCTKEVGGRQ LREGLQLREG LRNSKRRLEE AHQA

UniProtKB: Protein Jumonji

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Macromolecule #6: Zinc finger protein AEBP2

MacromoleculeName: Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.286885 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ISSTIMDVDS TISSGRSTPA MMNGQGSTTS SSKNIAYNCC WDQCQACFNS SPDLADHIRS IHVDGQRGGV FVCLWKGCKV YNTPSTSQS WLQRHMLTHS GDKPFKCVVG GCNASFASQG GLARHVPTHF SQQNSSKVSS QPKAKEESPS KAGMNKRRKL K NKRRRSLP ...String:
ISSTIMDVDS TISSGRSTPA MMNGQGSTTS SSKNIAYNCC WDQCQACFNS SPDLADHIRS IHVDGQRGGV FVCLWKGCKV YNTPSTSQS WLQRHMLTHS GDKPFKCVVG GCNASFASQG GLARHVPTHF SQQNSSKVSS QPKAKEESPS KAGMNKRRKL K NKRRRSLP RPHDFFDAQT LDAIRHRAIC FNLSAHIESL GKGHSVVFHS TVIAKRKEDS GKIKLLLHWM PEDILPDVWV NE SERHQLK TKVVHLSKLP KDTALLLDPN IYRTMPQKRL KR

UniProtKB: Zinc finger protein AEBP2

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Macromolecule #8: H3K36me3-modified histone H3

MacromoleculeName: H3K36me3-modified histone H3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.322774 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QLATKAARKS APATGGV(M3L)KP HR

UniProtKB: Histone H3.1

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Macromolecule #7: DNA (26-mer)

MacromoleculeName: DNA (26-mer) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.043523 KDa
SequenceString:
(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DC) (DA)(DG)(DC)

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Macromolecule #9: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.046153 KDa
SequenceString:
(DG)(DC)(DT)(DG)(DC)(DC)(DG)(DG)(DC)(DG) (DG)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)

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Macromolecule #10: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 10 / 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: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 1.8 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:

21707

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61193
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
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  • 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

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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

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