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- EMDB-43359: PRC2_AJ1-450 bound to H3K4me3 -

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Basic information

Entry
Database: EMDB / ID: EMD-43359
TitlePRC2_AJ1-450 bound to H3K4me3
Map data
Sample
  • Complex: PRC2_AJ1-450 bound to H3K4me3-modified nucleosome
    • Protein or peptide: SUZ12
    • Protein or peptide: JARID2
    • Protein or peptide: EZH2
    • Protein or peptide: Histone H3
    • Protein or peptide: EED
    • Protein or peptide: RBAP48
    • Protein or peptide: AEPB2
Keywordscomplex / methyltransferase / histone / epigenetics / GENE REGULATION
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 / sex chromatin / 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 / sex chromatin / CAF-1 complex / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / response to tetrachloromethane / primary miRNA binding / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle cell proliferation / facultative heterochromatin formation / ubiquitin-modified histone reader activity / positive regulation of cell cycle G1/S phase transition / negative regulation of cardiac muscle hypertrophy / NuRD complex / NURF 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 / negative regulation of stem cell differentiation / regulation of stem cell differentiation / RSC-type complex / pronucleus / chromatin silencing complex / protein-lysine N-methyltransferase activity / Polo-like kinase mediated events / cardiac muscle hypertrophy in response to stress / Transcription of E2F targets under negative control by DREAM complex / G1 to G0 transition / positive regulation of dendrite development / cardiac muscle cell proliferation / histone H3 methyltransferase activity / synaptic transmission, GABAergic / histone methyltransferase complex / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / histone methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / ATPase complex / negative regulation of gene expression, epigenetic / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / negative regulation of cell differentiation / positive regulation of protein serine/threonine kinase activity / subtelomeric heterochromatin formation / ribonucleoprotein complex binding / pericentric heterochromatin / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin E associated events during G1/S transition / Chromatin modifying enzymes / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding / Cyclin A:Cdk2-associated events at S phase entry / keratinocyte differentiation / spleen development / protein localization to chromatin / Regulation of TP53 Activity through Acetylation / : / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cytokine production involved in inflammatory response / telomere organization / positive regulation of GTPase activity / positive regulation of MAP kinase activity / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / B cell differentiation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / cellular response to leukemia inhibitory factor / DNA methylation / enzyme activator activity / Condensation of Prophase Chromosomes / negative regulation of cell migration / Chromatin modifications during the maternal to zygotic transition (MZT) / liver development / thymus development / HCMV Late Events / SIRT1 negatively regulates rRNA expression
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 / 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 / JmjC domain, hydroxylase / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / 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 / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / Zinc finger protein AEBP2 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43359.png

Downloads & links

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Map

FileDownload / File: emd_43359.map.gz / Format: CCP4 / Size: 411.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 476 pix.
= 409.36 Å		0.86 Å/pix.
x 476 pix.
= 409.36 Å		0.86 Å/pix.
x 476 pix.
= 409.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.196
Minimum - Maximum-1.1663883 - 1.670652
Average (Standard dev.)0.00043816795 (±0.03299722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions476476476
Spacing476476476
CellA=B=C: 409.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43359_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43359_half_map_2.map
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Sample components

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Entire : PRC2_AJ1-450 bound to H3K4me3-modified nucleosome

EntireName: PRC2_AJ1-450 bound to H3K4me3-modified nucleosome
Components
  • Complex: PRC2_AJ1-450 bound to H3K4me3-modified nucleosome
    • Protein or peptide: SUZ12
    • Protein or peptide: JARID2
    • Protein or peptide: EZH2
    • Protein or peptide: Histone H3
    • Protein or peptide: EED
    • Protein or peptide: RBAP48
    • Protein or peptide: AEPB2

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Supramolecule #1: PRC2_AJ1-450 bound to H3K4me3-modified nucleosome

SupramoleculeName: PRC2_AJ1-450 bound to H3K4me3-modified nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: SUZ12

MacromoleculeName: SUZ12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

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Macromolecule #2: JARID2

MacromoleculeName: JARID2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.021812 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNSQKRQHAE GIAGSLKTVN GLLGNDQSKG LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQR(M3L)FAQ SQPNSPSTTP VKIVEPLLPP PATQISDLSK RKPKTED FL TFLCLRGSPA ...String:
MSKERPKRNI IQKKYDDSDG IPWSEERVVR KVLYLSLKEF KNSQKRQHAE GIAGSLKTVN GLLGNDQSKG LGPASEQSEN EKDDASQVS STSNDVSSSD FEEGPSRKRP RLQAQR(M3L)FAQ SQPNSPSTTP VKIVEPLLPP PATQISDLSK RKPKTED FL TFLCLRGSPA LPNSMVYFGS SQDEEEVEEE DDETEDVKTA TNNASSSCQS TPRKGKTHKH VHNGHVFNGS SRSTREKE P VQKHKSKEAT PAKEKHSDHR ADSRREQASA NHPAAAPSTG SSAKGLAATH HHPPLHRSAQ DLRKQVSKVN GVTRMSSLG AGVTSAKKMR EVRPSPSKTV KYTATVTKGA VTYTKAKREL VKDTKPNHHK PSSAVNHTIS GKTESSNAKT RKQVLSLGGA SKSTGPAVN GLKVSGRLNP KSCTKEVGGR QLREGLQLRE GLRNSKRRLE EAHQAEKPQS PPKKMKGAAG PAEGPGKKAP A ERGLLNGH VKKEVPERSL ERNRPKRATA GKSTPGRQAH GKADSASCEN RSTSQPESVH KPQDSGKAEK GGGKAGWAAM DE IPVLRPS AKEFHDPLIY IESVRAQVEK FGMCRVIPPP DWRPECKLND EMRFVTQIQH IHKLGRRWGP NVQRLACIKK HLK SQGITM DELPLIGGCE LDLACFFRLI NEMGGMQQVT DLKKWNKLAD MLRIPRTAQD RLAKLQEAYC QYLLSYDSLS PEEH RRLEK EVLMEKEILE KRKGPLEGHT ENDHHKFHPL PRFEPKNGLI HGVAPRNGFR SKLKEVGQAQ LKTGRRRLFA QEKEV VKEE EEDKGVLNDF HKCIYKGRSV SLTTFYRTAR NIMSMCFSKE PAPAEIEQEY WRLVEEKDCH VAVHCGKVDT NTHGSG FPV GKSEPFSRHG WNLTVLPNNT GSILRHLGAV PGVTIPWLNI GMVFSTSCWS RDQNHLPYID YLHTGADCIW YCIPAEE EN KLEDVVHTLL QANGTPGLQM LESNVMISPE VLCKEGIKVH RTVQQSGQFV VCFPGSFVSK VCCGYSVSET VHFATTQW T SMGFETAKEM KRRHIAKPFS MEKLLYQIAQ AEAKKENGPT LSTISALLDE LRDTELRQRR QLFEAGLHSS ARYGSHDGS STVADGKKKP RKWLQLETSE RRCQICQHLC YLSMVVQENE NVVFCLECAL RHVEKQKSCR GLKLMYRYDE EQIISLVNQI CGKVSGKNG SIENCLSKPT PKRGPRKRAT VDVPPSRLSA SSSSKSASSS S

UniProtKB: Protein Jumonji

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Macromolecule #3: EZH2

MacromoleculeName: EZH2 / type: protein_or_peptide / ID: 3 / 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

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Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.280694 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QLATKAARKS APATGGVKKP HR

UniProtKB: Histone H3.1

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Macromolecule #5: EED

MacromoleculeName: EED / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: RBAP48

MacromoleculeName: RBAP48 / type: protein_or_peptide / ID: 6 / 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

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Macromolecule #7: AEPB2

MacromoleculeName: AEPB2 / 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

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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

Concentration0.28 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

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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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21707

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102257
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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  • 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

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