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- PDB-9c8u: Human PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min -

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Basic information

Entry
Database: PDB / ID: 9c8u
TitleHuman PRC2 - RvLEAM (short) (1:6 molar ratio), cross-linked 10 min
Components
  • (Polycomb protein ...) x 2
  • Isoform 2 of Histone-lysine N-methyltransferase EZH2
  • Protein Jumonji
  • RBAP48
  • Zinc finger protein AEBP2
KeywordsDNA BINDING PROTEIN / Human polycomb repressive complex 2 / RvLEAM / air-water-interface
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / CAF-1 complex / negative regulation of keratinocyte differentiation ...protein localization to pericentric heterochromatin / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / CAF-1 complex / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / primary miRNA binding / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of adaxial/abaxial pattern formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / negative regulation of cardiac muscle cell proliferation / histone H3K27 methyltransferase activity / sex chromatin / ubiquitin-modified histone reader activity / positive regulation of cell cycle G1/S phase transition / NuRD complex / NURF complex / facultative heterochromatin formation / regulation of cell fate specification / negative regulation of stem cell population maintenance / genomic imprinting / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / RSC-type complex / negative regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / cardiac muscle hypertrophy in response to stress / chromatin silencing complex / Transcription of E2F targets under negative control by DREAM complex / pronucleus / G1 to G0 transition / positive regulation of dendrite development / histone H3 methyltransferase activity / histone methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of G1/S transition of mitotic cell cycle / ATPase complex / spinal cord development / lncRNA binding / negative regulation of gene expression, epigenetic / synaptic transmission, GABAergic / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / histone methyltransferase complex / Transcriptional Regulation by E2F6 / pericentric heterochromatin / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of transcription elongation by RNA polymerase II / G0 and Early G1 / negative regulation of cell differentiation / : / cardiac muscle cell proliferation / positive regulation of protein serine/threonine kinase activity / positive regulation of MAP kinase activity / positive regulation of epithelial to mesenchymal transition / subtelomeric heterochromatin formation / 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 / nucleosome binding / keratinocyte differentiation / spleen development / protein localization to chromatin / Regulation of TP53 Activity through Acetylation / positive regulation of GTPase activity / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cytokine production involved in inflammatory response / B cell differentiation / SUMOylation of chromatin organization proteins / negative regulation of cell migration / thymus development / cellular response to leukemia inhibitory factor / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / ubiquitin binding / central nervous system development / PRC2 methylates histones and DNA / hippocampus development / transcription corepressor binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / transcription coregulator activity
Similarity search - Function
: / 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 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 profile. / Small domain found in the jumonji family of transcription factors / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / jmjN domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / JmjC domain, hydroxylase / SET domain superfamily / SET domain profile. / 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 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAbe, K.M. / Li, G. / He, Q. / Grant, T. / Lim, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM130550 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM131023 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM150023 United States
Citation
Journal: Nat Commun / Year: 2024
Title: Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.
Authors: Kaitlyn M Abe / Gan Li / Qixiang He / Timothy Grant / Ci Ji Lim /
Abstract: Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and ...Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Embryogenesis Abundant (LEA) proteins to withstand desiccation stress. Here we show that these LEA proteins, when used as additives during plunge freezing, effectively mitigate AWI damage to fragile multi-subunit molecular samples. The resulting high-resolution cryo-EM maps are comparable to or better than those obtained using existing AWI damage mitigation methods. Cryogenic electron tomography reveals that particles are localized at specific interfaces, suggesting LEA proteins form a barrier at the AWI. This interaction may explain the observed sample-dependent preferred orientation of particles. LEA proteins offer a simple, cost-effective, and adaptable approach for cryo-EM structural biologists to overcome AWI-related sample damage, potentially revitalizing challenging projects and advancing the field of structural biology.
#1: Journal: Science / Year: 2023
Title: Structural basis for inactivation of PRC2 by G-quadruplex RNA.
Authors: Jiarui Song / Anne R Gooding / Wayne O Hemphill / Brittney D Love / Anne Robertson / Liqi Yao / Leonard I Zon / Trista E North / Vignesh Kasinath / Thomas R Cech /
Abstract: Polycomb repressive complex 2 (PRC2) silences genes through trimethylation of histone H3K27. PRC2 associates with numerous precursor messenger RNAs (pre-mRNAs) and long noncoding RNAs (lncRNAs) with ...Polycomb repressive complex 2 (PRC2) silences genes through trimethylation of histone H3K27. PRC2 associates with numerous precursor messenger RNAs (pre-mRNAs) and long noncoding RNAs (lncRNAs) with a binding preference for G-quadruplex RNA. In this work, we present a 3.3-Å-resolution cryo-electron microscopy structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface composed of two copies of the catalytic subunit EZH2, thereby blocking nucleosome DNA interaction and histone H3 tail accessibility. Furthermore, an RNA-binding loop of EZH2 facilitates the handoff between RNA and DNA, another activity implicated in PRC2 regulation by RNA. We identified a gain-of-function mutation in this loop that activates PRC2 in zebrafish. Our results reveal mechanisms for RNA-mediated regulation of a chromatin-modifying enzyme.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 28, 2025Group: Data collection / Category: em_software / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Polycomb protein SUZ12
C: Polycomb protein EED
D: RBAP48
A: Isoform 2 of Histone-lysine N-methyltransferase EZH2
E: Protein Jumonji
F: Zinc finger protein AEBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,07113
Polymers295,6136
Non-polymers4587
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polycomb protein ... , 2 types, 2 molecules BC

#1: Protein Polycomb protein SUZ12 / Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor ...Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor of zeste 12 protein homolog


Mass: 83181.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022
#2: Protein Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 42386.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75530

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Protein , 3 types, 3 molecules DAF

#3: Protein RBAP48 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I 48 kDa subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 47709.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#4: Protein Isoform 2 of Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 86017.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15910, [histone H3]-lysine27 N-trimethyltransferase
#6: Protein Zinc finger protein AEBP2 / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 32881.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6ZN18

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Protein/peptide / Non-polymers , 2 types, 8 molecules E

#5: Protein/peptide Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 3436.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92833
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Polycomb Repressive Complex 2 / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 366459 / Symmetry type: POINT

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