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- EMDB-62475: Structure of human PRC2 with C36 compound -

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Basic information

Entry
Database: EMDB / ID: EMD-62475
TitleStructure of human PRC2 with C36 compound
Map dataCryo-EM map of human PRC2 with C36 compound
Sample
  • Complex: human PRC2 with C36 compound
    • Protein or peptide: Histone-lysine N-methyltransferase EZH2
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Zinc finger protein AEBP2
    • Protein or peptide: Histone-binding protein RBBP4
  • Ligand: 2-[2-[[4-[(8-chloranyl-1,7-naphthyridin-2-yl)amino]cyclohexyl]methylamino]pyrimidin-5-yl]-N-(oxetan-3-yl)ethanamide
KeywordsH3K27 methyltransferase / PRC2 / inhibitor / GENE REGULATION
Function / homology
Function and homology information


hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / regulation of kidney development / CAF-1 complex / negative regulation of keratinocyte differentiation / negative regulation of retinoic acid receptor signaling pathway ...hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / regulation of kidney development / CAF-1 complex / negative regulation of keratinocyte differentiation / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / cerebellar cortex development / primary miRNA binding / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / histone H3K27 methyltransferase activity / regulation of adaxial/abaxial pattern formation / random inactivation of X chromosome / sex chromatin / positive regulation of cell cycle G1/S phase transition / NURF complex / regulatory ncRNA-mediated heterochromatin formation / facultative heterochromatin formation / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / genomic imprinting / 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 / negative regulation of stem cell differentiation / regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / RSC-type complex / chromatin silencing complex / Transcription of E2F targets under negative control by DREAM complex / pronucleus / cardiac muscle hypertrophy in response to stress / positive regulation of dendrite development / histone H3K9me2/3 reader activity / histone H3 methyltransferase activity / G1 to G0 transition / histone methyltransferase activity / ATPase complex / negative regulation of G1/S transition of mitotic cell cycle / DNA methylation-dependent constitutive heterochromatin formation / G1/S-Specific Transcription / negative regulation of gene expression, epigenetic / positive regulation of MAP kinase activity / lncRNA binding / spinal cord development / Sin3-type complex / histone deacetylase complex / synaptic transmission, GABAergic / positive regulation of stem cell population maintenance / positive regulation of protein serine/threonine kinase activity / Transcriptional Regulation by E2F6 / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / negative regulation of transcription elongation by RNA polymerase II / G0 and Early G1 / positive regulation of GTPase activity / negative regulation of cell differentiation / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / pericentric heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / nucleosome binding / keratinocyte differentiation / Regulation of TP53 Activity through Acetylation / protein localization to chromatin / heterochromatin / negative regulation of cytokine production involved in inflammatory response / liver regeneration / Deposition of new CENPA-containing nucleosomes at the centromere / B cell differentiation / negative regulation of cell migration / SUMOylation of chromatin organization proteins / transcription corepressor binding / Regulation of PTEN gene transcription / stem cell differentiation / cellular response to leukemia inhibitory factor / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / hippocampus development / transcription coregulator activity / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / G1/S transition of mitotic cell cycle / protein-DNA complex / chromatin DNA binding / regulation of circadian rhythm
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 / : / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / 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 / 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-binding protein RBBP4 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Zinc finger protein AEBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsGao H / Cao T / Liu Y / Liu D / Yu H / Qi W
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271258 China
National Natural Science Foundation of China (NSFC)32130053 China
National Natural Science Foundation of China (NSFC)92253301 China
National Natural Science Foundation of China (NSFC)32270648 China
Ministry of Science and Technology (MoST, China)2023YFA0913404 China
CitationJournal: To Be Published
Title: Structure of human PRC2 with SAH and H3K27me3 peptide
Authors: Gao H / Cao T / Liu Y / Liu D / Yu H / Qi W
History
DepositionNov 20, 2024-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62475.png

Downloads & links

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Map

FileDownload / File: emd_62475.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of human PRC2 with C36 compound
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 387.72 Å		1.08 Å/pix.
x 360 pix.
= 387.72 Å		1.08 Å/pix.
x 360 pix.
= 387.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-2.2075756 - 3.5944867
Average (Standard dev.)0.0019769745 (±0.051395807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 387.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of human PRC2 with C36 compound

Fileemd_62475_half_map_1.map
AnnotationCryo-EM map of human PRC2 with C36 compound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of human PRC2 with C36 compound

Fileemd_62475_half_map_2.map
AnnotationCryo-EM map of human PRC2 with C36 compound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human PRC2 with C36 compound

EntireName: human PRC2 with C36 compound
Components
  • Complex: human PRC2 with C36 compound
    • Protein or peptide: Histone-lysine N-methyltransferase EZH2
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Zinc finger protein AEBP2
    • Protein or peptide: Histone-binding protein RBBP4
  • Ligand: 2-[2-[[4-[(8-chloranyl-1,7-naphthyridin-2-yl)amino]cyclohexyl]methylamino]pyrimidin-5-yl]-N-(oxetan-3-yl)ethanamide

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Supramolecule #1: human PRC2 with C36 compound

SupramoleculeName: human PRC2 with C36 compound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Histone-lysine N-methyltransferase EZH2

MacromoleculeName: Histone-lysine N-methyltransferase EZH2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine27 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.615453 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHHHMG QTGKKSEKGP VCWRKRVKSE YMRLRQLKRF RRADEVKSMF SSNRQKILER TEILNQEWKQ RRIQPVHILT SVSSLRGTR ECSVTSDLDF PTQVIPLKTL NAVASVPIMY SWSPLQQNFM VEDETVLHNI PYMGDEVLDQ DGTFIEELIK N YDGKVHGD ...String:
HHHHHHHHMG QTGKKSEKGP VCWRKRVKSE YMRLRQLKRF RRADEVKSMF SSNRQKILER TEILNQEWKQ RRIQPVHILT SVSSLRGTR ECSVTSDLDF PTQVIPLKTL NAVASVPIMY SWSPLQQNFM VEDETVLHNI PYMGDEVLDQ DGTFIEELIK N YDGKVHGD RECGFINDEI FVELVNALGQ YNDDDDDDDG DDPEEREEKQ KDLEDHRDDK ESRPPRKFPS DKIFEAISSM FP DKGTAEE LKEKYKELTE QQLPGALPDE CTPNIDGPNA KSVQREQSLH SFHTLFCRRC FKYDCFLHPF HATPNTYKRK NTE TALDNK PCGPQCYQHL EGAKEFAAAL TAERIKTPPK RPGGRRRGRL PNNSSRPSTP TINVLESKDT DSDREAGTET GGEN NDKEE EEKKDETSSS SEANSRCQTP IKMKPNIEPP ENVEWSGAEA SMFRVLIGTY YDNFCAIARL IGTKTCRQVY EFRVK ESSI IAPAPAEDVD TPPRKKKRKH RLWAAHCRKI QLKKDGSSNH VYNYQPCDHP RQPCDSSCPC VIAQNFCEKF CQCSSE CQN RFPGCRCKAQ CNTKQCPCYL AVRECDPDLC LTCGAADHWD SKNVSCKNCS IQRGSKKHLL LAPSDVAGWG IFIKDPV QK NEFISEYCGE IISQDEADRR GKVYDKYMCS FLFNLNNDFV VDATRKGNKI RFANHSVNPN CYAKVMMVNG DHRIGIFA K RAIQTGEELF FDYRYSQADA LKYVGIEREM EIP

UniProtKB: Histone-lysine N-methyltransferase EZH2

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Macromolecule #2: Polycomb protein EED

MacromoleculeName: Polycomb protein EED / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.199664 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHHHMS EREVSTAPAG TDMPAAKKQK LSSDENSNPD LSGDENDDAV SIESGTNTER PDTPTNTPNA PGRKSWGKGK WKSKKCKYL FKCVNSLKED HNQPLFGVQF NWHSKEGDPL VFATVGSNRV TLYECHSQGE IRLLQSYVDA DADENFYTCA W TYDSNTSH ...String:
HHHHHHHHMS EREVSTAPAG TDMPAAKKQK LSSDENSNPD LSGDENDDAV SIESGTNTER PDTPTNTPNA PGRKSWGKGK WKSKKCKYL FKCVNSLKED HNQPLFGVQF NWHSKEGDPL VFATVGSNRV TLYECHSQGE IRLLQSYVDA DADENFYTCA W TYDSNTSH PLLAVAGSRG IIRIINPITM QCIKHYVGHG NAINELKFHP RDPNLLLSVS KDHALRLWNI QTDTLVAIFG GV EGHRDEV LSADYDLLGE KIMSCGMDHS LKLWRINSKR MMNAIKESYD YNPNKTNRPF ISQKIHFPDF STRDIHRNYV DCV RWLGDL ILSKSCENAI VCWKPGKMED DIDKIKPSES NVTILGRFDY SQCDIWYMRF SMDFWQKMLA LGNQVGKLYV WDLE VEDPH KAKCTTLTHH KCGAAIRQTS FSRDSSILIA VCDDASIWRW DRA

UniProtKB: Polycomb protein EED

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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: 70.049672 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: FLQAFEKPTQ IYRFLRTRNL IAPIFLHRTL TYMSHRNSRT NIKRKTFKVD DMLSKVEKMK GEQESHSLSA HLQLTFTGFF HKNDKPSPN SENEQNSVTL EVLLVKVCHK KRKDVSCPIR QVPTGKKQVP LNPDLNQTKP GNFPSLAVSS NEFEPSNSHM V KSYSLLFR ...String:
FLQAFEKPTQ IYRFLRTRNL IAPIFLHRTL TYMSHRNSRT NIKRKTFKVD DMLSKVEKMK GEQESHSLSA HLQLTFTGFF HKNDKPSPN SENEQNSVTL EVLLVKVCHK KRKDVSCPIR QVPTGKKQVP LNPDLNQTKP GNFPSLAVSS NEFEPSNSHM V KSYSLLFR VTRPGRREFN GMINGETNEN IDVNEELPAR RKRNREDGEK TFVAQMTVFD KNRRLQLLDG EYEVAMQEME EC PISKKRA TWETILDGKR LPPFETFSQG PTLQFTLRWT GETNDKSTAP IAKPLATRNS ESLHQENKPG SVKPTQTIAV KES LTTDLQ TRKEKDTPNE NRQKLRIFYQ FLYNNNTRQQ TEARDDLHCP WCTLNCRKLY SLLKHLKLCH SRFIFNYVYH PKGA RIDVS INECYDGSYA GNPQDIHRQP GFAFSRNGPV KRTPITHILV CRPKRTKASM SEFLESEDGE VEQQRTYSSG HNRLY FHSD TCLPLRPQEM EVDSEDEKDP EWLREKTITQ IEEFSDVNEG EKEVMKLWNL HVMKHGFIAD NQMNHACMLF VENYGQ KII KKNLCRNFML HLVSMHDFNL ISIMSIDKAV TKLREMQ

UniProtKB: Polycomb protein SUZ12

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Macromolecule #4: Zinc finger protein AEBP2

MacromoleculeName: Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.23619 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
PHDFFDAQTL DAIRHRAICF NLSAHIESLG KGHSVVFHST VIAKRKEDSG KIKLLLHWMP EDILPDVWVN ESERHQLKTK VVHLSKLPK DTALLLDPNI YRTMPQK

UniProtKB: Zinc finger protein AEBP2

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Macromolecule #5: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.89277 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: KEAAFDDAVE ERVINEEYKI WKKNTPFLYD LVMTHALEWP SLTAQWLPDV TRPEGKDFSI HRLVLGTHTS DEQNHLVIAS VQLPNDDAQ FDASHYDSEK GEFGGFGSVS GKIEIEIKIN HEGEVNRARY MPQNPCIIAT KTPSSDVLVF DYTKHPSKPD P SGECNPDL ...String:
KEAAFDDAVE ERVINEEYKI WKKNTPFLYD LVMTHALEWP SLTAQWLPDV TRPEGKDFSI HRLVLGTHTS DEQNHLVIAS VQLPNDDAQ FDASHYDSEK GEFGGFGSVS GKIEIEIKIN HEGEVNRARY MPQNPCIIAT KTPSSDVLVF DYTKHPSKPD P SGECNPDL RLRGHQKEGY GLSWNPNLSG HLLSASDDHT ICLWDISAVP KEGKVVDAKT IFTGHTAVVE DVSWHLLHES LF GSVADDQ KLMIWDTRSN NTSKPSHSVD AHTAEVNCLS FNPYSEFILA TGSADKTVAL WDLRNLKLKL HSFESHKDEI FQV QWSPHN ETILASSGTD RRLNVWDLSK IGEEQSPEDA EDGPPELLFI HGGHTAKISD FSWNPNEPWV ICSVSEDNIM QVWQ MAENI YN

UniProtKB: Histone-binding protein RBBP4

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Macromolecule #6: 2-[2-[[4-[(8-chloranyl-1,7-naphthyridin-2-yl)amino]cyclohexyl]met...

MacromoleculeName: 2-[2-[[4-[(8-chloranyl-1,7-naphthyridin-2-yl)amino]cyclohexyl]methylamino]pyrimidin-5-yl]-N-(oxetan-3-yl)ethanamide
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1EGC
Molecular weightTheoretical: 481.978 Da

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.4) / Number images used: 67922
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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