[English] 日本語
Yorodumi
- EMDB-43357: PRC2_AJ119-450 bound to H3K4me3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43357
TitlePRC2_AJ119-450 bound to H3K4me3
Map data
Sample
  • Complex: PRC2_AJ119-450 bound to H3K4me3-modified nucleosome
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: EZH2
    • Protein or peptide: Protein Jumonji
    • Protein or peptide: Isoform 3 of Zinc finger protein AEBP2
    • Protein or peptide: Histone H3.1t
  • Ligand: ZINC ION
Keywordscomplex / methyltransferase / histone / epigenetics / GENE REGULATION
Function / homology
Function and homology information


regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / spermatogonial cell division / CAF-1 complex / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / primary miRNA binding / histone H3K27 methyltransferase activity / RSC-type complex / ubiquitin-modified histone reader activity ...regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / spermatogonial cell division / CAF-1 complex / negative regulation of retinoic acid receptor signaling pathway / histone H3K27 trimethyltransferase activity / primary miRNA binding / histone H3K27 methyltransferase activity / RSC-type complex / ubiquitin-modified histone reader activity / 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 / DNA replication-dependent chromatin assembly / 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 / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / chromatin silencing complex / Transcription of E2F targets under negative control by DREAM complex / pronucleus / positive regulation of dendrite development / histone H3K9me2/3 reader activity / positive regulation of protein serine/threonine kinase activity / histone H3 methyltransferase activity / spinal cord development / synaptic transmission, GABAergic / histone methyltransferase activity / negative regulation of gene expression, epigenetic / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / positive regulation of MAP kinase activity / histone deacetylase complex / lncRNA binding / histone methyltransferase complex / Transcriptional Regulation by E2F6 / negative regulation of cell differentiation / RNA Polymerase I Transcription Initiation / G0 and Early G1 / subtelomeric heterochromatin formation / positive regulation of GTPase activity / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / Cyclin E associated events during G1/S transition / pericentric heterochromatin / 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 / nucleosome binding / stem cell differentiation / Chromatin modifying enzymes / heterochromatin / negative regulation of cytokine production involved in inflammatory response / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of cell migration / telomere organization / Interleukin-7 signaling / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / negative regulation of transforming growth factor beta receptor signaling pathway / hippocampus development / RNA Polymerase I Promoter Opening / transcription corepressor binding / Inhibition of DNA recombination at telomere / Regulation of PTEN gene transcription / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / condensed nuclear chromosome / DNA methylation / Condensation of Prophase Chromosomes / central nervous system development / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / brain development / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / ubiquitin binding / HDACs deacetylate histones / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ)
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 superfamily / SET domain / 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 / Histone H3.1t / 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 15, 2025-
Map releaseJan 15, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43357.png

Downloads & links

-
Map

FileDownload / File: emd_43357.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: 0.36
Minimum - Maximum-3.391215 - 5.0086713
Average (Standard dev.)0.0016910427 (±0.061914705)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_43357_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43357_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : PRC2_AJ119-450 bound to H3K4me3-modified nucleosome

EntireName: PRC2_AJ119-450 bound to H3K4me3-modified nucleosome
Components
  • Complex: PRC2_AJ119-450 bound to H3K4me3-modified nucleosome
    • Protein or peptide: Polycomb protein EED
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Polycomb protein SUZ12
    • Protein or peptide: Histone-binding protein RBBP4
    • Protein or peptide: EZH2
    • Protein or peptide: Protein Jumonji
    • Protein or peptide: Isoform 3 of Zinc finger protein AEBP2
    • Protein or peptide: Histone H3.1t
  • Ligand: ZINC ION

+
Supramolecule #1: PRC2_AJ119-450 bound to H3K4me3-modified nucleosome

SupramoleculeName: PRC2_AJ119-450 bound to H3K4me3-modified nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

+
Macromolecule #1: Polycomb protein EED

MacromoleculeName: Polycomb protein EED / type: protein_or_peptide / ID: 1 / 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

+
Macromolecule #2: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 747.883 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ART(M3L)QT

UniProtKB: Histone H3.1

+
Macromolecule #3: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.181922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN ...String:
MAPQKHGGGG GGGSGPSAGS GGGGFGGSAA VAAATASGGK SGGGSCGGGG SYSASSSSSA AAAAGAAVLP VKKPKMEHVQ ADHELFLQA FEKPTQIYRF LRTRNLIAPI FLHRTLTYMS HRNSRTNIKR KTFKVDDMLS KVEKMKGEQE SHSLSAHLQL T FTGFFHKN DKPSPNSENE QNSVTLEVLL VKVCHKKRKD VSCPIRQVPT GKKQVPLNPD LNQTKPGNFP SLAVSSNEFE PS NSHMVKS YSLLFRVTRP GRREFNGMIN GETNENIDVN EELPARRKRN REDGEKTFVA QMTVFDKNRR LQLLDGEYEV AMQ EMEECP ISKKRATWET ILDGKRLPPF ETFSQGPTLQ FTLRWTGETN DKSTAPIAKP LATRNSESLH QENKPGSVKP TQTI AVKES LTTDLQTRKE KDTPNENRQK LRIFYQFLYN NNTRQQTEAR DDLHCPWCTL NCRKLYSLLK HLKLCHSRFI FNYVY HPKG ARIDVSINEC YDGSYAGNPQ DIHRQPGFAF SRNGPVKRTP ITHILVCRPK RTKASMSEFL ESEDGEVEQQ RTYSSG HNR LYFHSDTCLP LRPQEMEVDS EDEKDPEWLR EKTITQIEEF SDVNEGEKEV MKLWNLHVMK HGFIADNQMN HACMLFV EN YGQKIIKKNL CRNFMLHLVS MHDFNLISIM SIDKAVTKLR EMQQKLEKGE SASPANEEIT EEQNGTANGF SEINSKEK A LETDSVSGVS KQSKKQKL

UniProtKB: Polycomb protein SUZ12

+
Macromolecule #4: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 4 / 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

+
Macromolecule #5: EZH2

MacromoleculeName: EZH2 / type: protein_or_peptide / ID: 5 / 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

+
Macromolecule #6: Protein Jumonji

MacromoleculeName: Protein Jumonji / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 138.979719 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNSQKRQHAE GIAGSLKTVN GLLGNDQSKG LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQRKFAQ SQPNSPSTTP VKIVEPLLPP PATQISDLSK RKPKTEDFLT F LCLRGSPA ...String:
MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNSQKRQHAE GIAGSLKTVN GLLGNDQSKG LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQRKFAQ SQPNSPSTTP VKIVEPLLPP PATQISDLSK RKPKTEDFLT F LCLRGSPA LPNSMVYFGS SQDEEEVEEE DDETEDVKTA TNNASSSCQS TPRKGKTHKH VHNGHVFNGS SRSTREKEPV QK HKSKEAT PAKEKHSDHR ADSRREQASA NHPAAAPSTG SSAKGLAATH HHPPLHRSAQ DLRKQVSKVN GVTRMSSLGA GVT SAKKMR EVRPSPSKTV KYTATVTKGA VTYTKAKREL VKDTKPNHHK PSSAVNHTIS GKTESSNAKT RKQVLSLGGA SKST GPAVN GLKVSGRLNP KSCTKEVGGR QLREGLQLRE GLRNSKRRLE EAHQAEKPQS PPKKMKGAAG PAEGPGKKAP AERGL LNGH VKKEVPERSL ERNRPKRATA GKSTPGRQAH GKADSASCEN RSTSQPESVH KPQDSGKAEK GGGKAGWAAM DEIPVL RPS AKEFHDPLIY IESVRAQVEK FGMCRVIPPP DWRPECKLND EMRFVTQIQH IHKLGRRWGP NVQRLACIKK HLKSQGI TM DELPLIGGCE LDLACFFRLI NEMGGMQQVT DLKKWNKLAD MLRIPRTAQD RLAKLQEAYC QYLLSYDSLS PEEHRRLE K EVLMEKEILE KRKGPLEGHT ENDHHKFHPL PRFEPKNGLI HGVAPRNGFR SKLKEVGQAQ LKTGRRRLFA QEKEVVKEE EEDKGVLNDF HKCIYKGRSV SLTTFYRTAR NIMSMCFSKE PAPAEIEQEY WRLVEEKDCH VAVHCGKVDT NTHGSGFPVG KSEPFSRHG WNLTVLPNNT GSILRHLGAV PGVTIPWLNI GMVFSTSCWS RDQNHLPYID YLHTGADCIW YCIPAEEENK L EDVVHTLL QANGTPGLQM LESNVMISPE VLCKEGIKVH RTVQQSGQFV VCFPGSFVSK VCCGYSVSET VHFATTQWTS MG FETAKEM KRRHIAKPFS MEKLLYQIAQ AEAKKENGPT LSTISALLDE LRDTELRQRR QLFEAGLHSS ARYGSHDGSS TVA DGKKKP RKWLQLETSE RRCQICQHLC YLSMVVQENE NVVFCLECAL RHVEKQKSCR GLKLMYRYDE EQIISLVNQI CGKV SGKNG SIENCLSKPT PKRGPRKRAT VDVPPSRLSA SSSSKSASSS S

UniProtKB: Protein Jumonji

+
Macromolecule #7: Isoform 3 of Zinc finger protein AEBP2

MacromoleculeName: Isoform 3 of Zinc finger protein AEBP2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.042133 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MYTRRYSSIS STIMDVDSTI SSGRSTPAMM NGQGSTTSSS KNIAYNCCWD QCQACFNSSP DLADHIRSIH VDGQRGGVFV CLWKGCKVY NTPSTSQSWL QRHMLTHSGD KPFKCVVGGC NASFASQGGL ARHVPTHFSQ QNSSKVSSQP KAKEESPSKA G MNKRRKLK ...String:
MYTRRYSSIS STIMDVDSTI SSGRSTPAMM NGQGSTTSSS KNIAYNCCWD QCQACFNSSP DLADHIRSIH VDGQRGGVFV CLWKGCKVY NTPSTSQSWL QRHMLTHSGD KPFKCVVGGC NASFASQGGL ARHVPTHFSQ QNSSKVSSQP KAKEESPSKA G MNKRRKLK NKRRRSLPRP HDFFDAQTLD AIRHRAICFN LSAHIESLGK GHSVVFHSTV IAKRKEDSGK IKLLLHWMPE DI LPDVWVN ESERHQLKTK VVHLSKLPKD TALLLDPNIY RTMPQKRLKR TLIRKVFNLY LSKQ

UniProtKB: Zinc finger protein AEBP2

+
Macromolecule #8: Histone H3.1t

MacromoleculeName: Histone H3.1t / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.987336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARKSAPATGG VKKPHRYR

UniProtKB: Histone H3.1t

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.28 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

-
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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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: 108372
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more