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- PDB-6c24: Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in ... -

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Entry
Database: PDB / ID: 6c24
TitleCryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Extended Active State
Components
  • (Polycomb protein ...) x 2
  • (Protein Jumonji) x 2
  • Histone-binding protein RBBP4
  • Histone-lysine N-methyltransferase EZH2
  • JARID2-substrate
  • SUZ12
  • Zinc finger protein AEBP2
KeywordsGENE REGULATION / polycomb repressive complex / AEBP2 / JARID2 / histone modification
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / negative regulation of keratinocyte differentiation / CAF-1 complex ...protein localization to pericentric heterochromatin / hepatocyte homeostasis / regulation of kidney development / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / negative regulation of keratinocyte differentiation / CAF-1 complex / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / ubiquitin-modified histone reader activity / response to tetrachloromethane / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / cerebellar cortex development / random inactivation of X chromosome / primary miRNA binding / regulatory ncRNA-mediated heterochromatin formation / histone H3K27 methyltransferase activity / facultative heterochromatin formation / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / positive regulation of cell cycle G1/S phase transition / 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 / chromatin silencing complex / regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / RSC-type complex / negative regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / pronucleus / cardiac muscle hypertrophy in response to stress / Polo-like kinase mediated events / synaptic transmission, GABAergic / positive regulation of dendrite development / histone H3 methyltransferase activity / cardiac muscle cell proliferation / lncRNA binding / histone methyltransferase complex / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / G1 to G0 transition / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / ATPase complex / histone methyltransferase activity / Sin3-type complex / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of cell differentiation / G0 and Early G1 / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / pericentric heterochromatin / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of epithelial to mesenchymal transition / Cyclin A:Cdk2-associated events at S phase entry / spleen development / keratinocyte differentiation / Deposition of new CENPA-containing nucleosomes at the centromere / protein localization to chromatin / Regulation of TP53 Activity through Acetylation / enzyme activator activity / methylated histone binding / SUMOylation of chromatin organization proteins / B cell differentiation / liver development / positive regulation of GTPase activity / transcription corepressor binding / thymus development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / ubiquitin binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / hippocampus development / central nervous system development / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / stem cell differentiation / HDACs deacetylate histones / promoter-specific chromatin binding / liver regeneration / transcription coregulator activity
Similarity search - Function
: / 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 ...: / 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 / 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 / JmjC domain, hydroxylase / SANT/Myb domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / A domain family that is part of the cupin metalloenzyme superfamily. / zinc finger / JmjC domain / JmjC domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / Mainly Beta
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: 3.5 Å
AuthorsKasinath, V. / Faini, M. / Poepsel, S. / Reif, D. / Feng, A. / Stjepanovic, G. / Aebersold, R. / Nogales, E.
Funding support United States, European Union, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
European Research Council (ERC)233226European Union
European Research Council (ERC)670821European Union
CitationJournal: Science / Year: 2018
Title: Structures of human PRC2 with its cofactors AEBP2 and JARID2.
Authors: Vignesh Kasinath / Marco Faini / Simon Poepsel / Dvir Reif / Xinyu Ashlee Feng / Goran Stjepanovic / Ruedi Aebersold / Eva Nogales /
Abstract: Transcriptionally repressive histone H3 lysine 27 methylation by Polycomb repressive complex 2 (PRC2) is essential for cellular differentiation and development. Here we report cryo-electron ...Transcriptionally repressive histone H3 lysine 27 methylation by Polycomb repressive complex 2 (PRC2) is essential for cellular differentiation and development. Here we report cryo-electron microscopy structures of human PRC2 in a basal state and two distinct active states while in complex with its cofactors JARID2 and AEBP2. Both cofactors mimic the binding of histone H3 tails. JARID2, methylated by PRC2, mimics a methylated H3 tail to stimulate PRC2 activity, whereas AEBP2 interacts with the RBAP48 subunit, mimicking an unmodified H3 tail. SUZ12 interacts with all other subunits within the assembly and thus contributes to the stability of the complex. Our analysis defines the complete architecture of a functionally relevant PRC2 and provides a structural framework to understand its regulation by cofactors, histone tails, and RNA.
History
DepositionJan 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 3, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.6Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: Polycomb protein SUZ12
B: Protein Jumonji
E: Protein Jumonji
K: Histone-lysine N-methyltransferase EZH2
L: Polycomb protein EED
M: Polycomb protein SUZ12
N: Histone-binding protein RBBP4
O: JARID2-substrate
P: Zinc finger protein AEBP2
Q: Polycomb protein SUZ12
Z: SUZ12
C: Histone-lysine N-methyltransferase EZH2


Theoretical massNumber of molelcules
Total (without water)639,13412
Polymers639,13412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polycomb protein ... , 2 types, 4 molecules AMQL

#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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15022
#5: 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: 50267.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75530

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Protein , 6 types, 7 molecules BEKCNPZ

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


Mass: 37706.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92833
#3: Protein Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 37664.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92833
#4: Protein Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 85492.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q15910, histone-lysine N-methyltransferase
#6: Protein Histone-binding protein RBBP4 / 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 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q09028
#8: Protein Zinc finger protein AEBP2 / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 33012.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZN18
#9: Protein SUZ12


Mass: 11507.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

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Protein/peptide , 1 types, 1 molecules O

#7: Protein/peptide JARID2-substrate


Mass: 735.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

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Details

Sequence detailsauthors have indicated that the macromolecule name is corresponding to chain Z is SUZ12. The ...authors have indicated that the macromolecule name is corresponding to chain Z is SUZ12. The expected sequence for this portion is: SUZ12 aa 150 - 356 SHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQ

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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: Ternary complex of PRC2 with cofactors AEBP2 and JARID2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.9
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: Volta Phase Plate

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249696 / Symmetry type: POINT
RefinementResolution: 3.5→151.2 Å / Cor.coef. Fo:Fc: 0.843 / SU B: 29.608 / SU ML: 0.428 / ESU R: 0.808
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.35739 --
obs0.35739 85373 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.285 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å2-2.76 Å2-7.99 Å2
2---5.7 Å20.19 Å2
3---3.1 Å2
Refinement stepCycle: 1 / Total: 13350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01913651
ELECTRON MICROSCOPYr_bond_other_d0.0040.0212530
ELECTRON MICROSCOPYr_angle_refined_deg1.4631.93318545
ELECTRON MICROSCOPYr_angle_other_deg1.005328657
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.36651747
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.08223.694582
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.712152067
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.9221578
ELECTRON MICROSCOPYr_chiral_restr0.0830.22077
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02115664
ELECTRON MICROSCOPYr_gen_planes_other0.0020.023214
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.30711.7977063
ELECTRON MICROSCOPYr_mcbond_other6.2911.7967062
ELECTRON MICROSCOPYr_mcangle_it10.96117.6548785
ELECTRON MICROSCOPYr_mcangle_other10.96417.6568786
ELECTRON MICROSCOPYr_scbond_it6.2611.9126588
ELECTRON MICROSCOPYr_scbond_other6.2611.9146589
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other11.14617.6739761
ELECTRON MICROSCOPYr_long_range_B_refined21.49151487
ELECTRON MICROSCOPYr_long_range_B_other21.49151488
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.49 6323 -
Rfree-0 -
obs--100 %

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