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- PDB-6c23: Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in ... -

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Entry
Database: PDB / ID: 6c23
TitleCryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State
Components
  • (Polycomb protein ...Polycomb-group proteins) 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 / homologyCXC domain / Tesmin/TSO1-like CXC domain / Trp-Asp (WD) repeats signature. / Zinc finger C2H2 type domain signature. / Histone-binding protein RBBP4 or subunit C of CAF1 complex / WD repeat binding protein EZH2 / C5HC2 zinc finger / jmjN domain / JmjC domain, hydroxylase / ARID/BRIGHT DNA binding domain ...CXC domain / Tesmin/TSO1-like CXC domain / Trp-Asp (WD) repeats signature. / Zinc finger C2H2 type domain signature. / Histone-binding protein RBBP4 or subunit C of CAF1 complex / WD repeat binding protein EZH2 / C5HC2 zinc finger / jmjN domain / JmjC domain, hydroxylase / ARID/BRIGHT DNA binding domain / SET domain / WD domain, G-beta repeat / Polycomb protein EED / ARID DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Zinc finger C2H2 superfamily / CXC domain / Zinc finger C2H2 type domain profile. / Zinc finger, C5HC2-type / SANT/Myb domain / SET domain / ARID DNA-binding domain / WD40 repeat / JmjC domain / JmjN domain / Zinc finger C2H2-type / Histone-binding protein RBBP4, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / WD40-repeat-containing domain / Polycomb protein, VEFS-Box / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Histone-lysine N-methyltransferase EZH1/EZH2 / Trp-Asp (WD) repeats profile. / VEFS-Box of polycomb protein / SET domain profile. / SUMOylation of chromatin organization proteins / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / G0 and Early G1 / Trp-Asp (WD) repeats circular profile. / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / HDACs deacetylate histones / PKMTs methylate histone lysines / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Activation of E2F1 target genes at G1/S / CXC domain profile. / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase I Transcription Initiation / Regulation of PTEN gene transcription / Transcriptional Regulation by E2F6 / Polycomb repressive complex 2 tri-helical domain / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / JmjC domain profile. / JmjN domain profile. / ARID domain profile. / histone H3-K4 demethylation, trimethyl-H3-K4-specific / negative regulation of histone methylation / response to tetrachloromethane / hepatocyte homeostasis / negative regulation of striated muscle cell differentiation / cellular response to trichostatin A / negative regulation of epidermal cell differentiation / histone H3-K27 trimethylation / CAF-1 complex / regulation of gliogenesis / cerebellar cortex development / G1 to G0 transition / NURF complex / regulation of adaxial/abaxial pattern formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / RSC-type complex / negative regulation of retinoic acid receptor signaling pathway / positive regulation of dendrite development / positive regulation of cell cycle G1/S phase transition / histone H3-K27 methylation / histone methyltransferase activity (H3-K27 specific) / primary miRNA binding / sex chromatin / positive regulation of histone H3-K9 methylation / negative regulation of transcription elongation from RNA polymerase II promoter / negative regulation of cardiac muscle hypertrophy / positive regulation of histone H3-K27 methylation / ESC/E(Z) complex / histone ubiquitination / negative regulation of cardiac muscle cell proliferation / regulation of gene expression by genetic imprinting / cardiac muscle hypertrophy in response to stress / protein-lysine N-methyltransferase activity / ATP-dependent chromatin remodeling / histone methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / histone methylation / DNA methylation / NuRD complex
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsKasinath, V. / Faini, M. / Poepsel, S. / Reif, D. / Feng, A. / Stjepanovic, G. / Aebersold, R. / Nogales, E.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 5, 2018 / Release: Jan 24, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 24, 2018Structure modelrepositoryInitial release
1.1Jan 31, 2018Structure modelDatabase referencescitation / citation_author_citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Feb 14, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.3Mar 7, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.4Oct 3, 2018Structure modelData collection / Refinement descriptionrefine

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Structure visualization

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Assembly

Deposited unit
A: Polycomb protein SUZ12
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
B: Protein Jumonji


Theoretical massNumber of molelcules
Total (without water)639,40612
Polyers639,40612
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein/peptide Polycomb protein SUZ12 / Polycomb-group proteins / 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: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15022
#4: Protein/peptide Polycomb protein EED / Polycomb-group proteins / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 50267.691 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75530

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Protein/peptide , 7 types, 8 molecules EKCNOPZB

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


Mass: 37936.629 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92833
#3: Protein/peptide 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: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q15910, histone-lysine N-methyltransferase
#5: Protein/peptide Histone-binding protein RBBP4 / 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: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09028
#6: Protein/peptide JARID2-substrate


Mass: 735.874 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#7: Protein/peptide Zinc finger protein AEBP2 / / Adipocyte enhancer-binding protein 2 / AE-binding protein 2


Mass: 33012.668 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZN18
#8: Protein/peptide SUZ12


Mass: 11507.176 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#9: Protein/peptide Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 37706.449 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: JARID2, JMJ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92833

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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 / 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: 1,2,3,4,5,6,7,8,9 / 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
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
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 145592 / Symmetry type: POINT
RefineCorrelation coeff Fo to Fc: 0.825 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 38.798 / Overall SU ML: 0.506 / Overall ESU R: 1.593
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 120.59 Å2 / Aniso B11: 3.83 Å2 / Aniso B12: -3.14 Å2 / Aniso B13: -8.51 Å2 / Aniso B22: -7.3 Å2 / Aniso B23: 1 Å2 / Aniso B33: 3.46 Å2
Least-squares processR factor R work: 0.35639 / R factor obs: 0.35639 / Highest resolution: 3.9 Å / Lowest resolution: 147.84 Å / Number reflection obs: 64175 / Percent reflection obs: 1
Number of atoms included #1Total: 13478
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01913784
ELECTRON MICROSCOPYr_bond_other_d0.0020.02012439
ELECTRON MICROSCOPYr_angle_refined_deg1.4971.93218761
ELECTRON MICROSCOPYr_angle_other_deg1.0083.00028406
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.0915.0001800
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.83723.831569
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.91215.0001986
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.97215.00070
ELECTRON MICROSCOPYr_chiral_restr0.0860.2002115
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02115973
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0203227
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_it7.92812.7807269
ELECTRON MICROSCOPYr_mcbond_other7.92712.7807268
ELECTRON MICROSCOPYr_mcangle_it13.61419.1349046
ELECTRON MICROSCOPYr_mcangle_other13.61319.1359047
ELECTRON MICROSCOPYr_scbond_it8.13412.6356515
ELECTRON MICROSCOPYr_scbond_other8.13412.6356516
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other14.22118.8029715
ELECTRON MICROSCOPYr_long_range_B_refined25.84853192
ELECTRON MICROSCOPYr_long_range_B_other25.85053182
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.9 Å / R factor R work: 0.463 / Lowest resolution: 4.001 Å / Number reflection R free: 0 / Number reflection R work: 4779 / Total number of bins used: 20 / Percent reflection obs: 1

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