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- EMDB-11910: Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. -

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Basic information

Entry
Database: EMDB / ID: EMD-11910
TitleHistone H3 recognition by nucleosome-bound PRC2 subunit EZH2.
Map dataShows the Relion 3.0 postprocessed cryo-EM map of the EZH2sub-Nucsub structure, generated by particle subtraction and focused 3D refinement.
Sample
  • Complex: EM map of EZH2 on nucleosome obtained from signal particle subtraction and focused refinement on PHF1-PRC2:dinucleosome map.
    • Complex: SUZ12 and EZH2
      • Protein or peptide: Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2
      • Protein or peptide: Polycomb protein SUZ12
    • Complex: Histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: Widom601 DNA plus linker
      • DNA: Widom601 DNA plus linker
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsPolycomb / nucleosome / histone methyltransferase / PRC2 / EZH2 / H3K36 / H3 tail / gene regulation / H3 / histone H3 / Polycomb Repressive Complex 2 / cryo-EM / nucleosome recognition / H3K36me2 / H3K36me3
Function / homology
Function and homology information


negative regulation of epidermal cell differentiation / : / : / transcription corepressor binding => GO:0001222 / subtelomeric heterochromatin formation => GO:0031509 / : / : / : / regulation of kidney development / hepatocyte homeostasis ...negative regulation of epidermal cell differentiation / : / : / transcription corepressor binding => GO:0001222 / subtelomeric heterochromatin formation => GO:0031509 / : / : / : / regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / random inactivation of X chromosome / primary miRNA binding / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / facultative heterochromatin formation / histone H3K27 methyltransferase activity / positive regulation of cell cycle G1/S phase transition / chromatin => GO:0000785 / negative regulation of G0 to G1 transition / chromatin silencing complex / ESC/E(Z) complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / RSC-type complex / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / negative regulation of cell differentiation / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / ribonucleoprotein complex binding / heterochromatin formation / positive regulation of epithelial to mesenchymal transition / keratinocyte differentiation / protein localization to chromatin / enzyme activator activity / methylated histone binding / SUMOylation of chromatin organization proteins / B cell differentiation / transcription corepressor binding / positive regulation of GTPase activity / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / stem cell differentiation / liver regeneration / hippocampus development / promoter-specific chromatin binding / positive regulation of MAP kinase activity / protein modification process / positive regulation of protein serine/threonine kinase activity / regulation of circadian rhythm / negative regulation of DNA-binding transcription factor activity / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / HCMV Early Events / G1/S transition of mitotic cell cycle / structural constituent of chromatin / transcription corepressor activity / nucleosome / rhythmic process / nucleosome assembly / response to estradiol / chromatin organization / methylation / Oxidative Stress Induced Senescence / cell population proliferation / chromosome, telomeric region / nuclear body / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / synapse / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription
Similarity search - Function
EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / 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 / : / Ezh2, MCSS domain / 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 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain / CXC domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SET domain profile. / SET domain / SANT/Myb domain / Zinc finger C2H2 type domain signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Histone-lysine N-methyltransferase EZH2 / Histone H2A
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsFinogenova K / Benda C
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1064 Germany
Max Planck Society Germany
CitationJournal: Elife / Year: 2020
Title: Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3.
Authors: Ksenia Finogenova / Jacques Bonnet / Simon Poepsel / Ingmar B Schäfer / Katja Finkl / Katharina Schmid / Claudia Litz / Mike Strauss / Christian Benda / Jürg Müller /
Abstract: Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 ...Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes . Accordingly, H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.
History
DepositionOct 29, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0328
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0328
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7at8
  • Surface level: 0.0328
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11910.png

Downloads & links

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Map

FileDownload / File: emd_11910.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationShows the Relion 3.0 postprocessed cryo-EM map of the EZH2sub-Nucsub structure, generated by particle subtraction and focused 3D refinement.
Voxel sizeX=Y=Z: 1.746 Å
Density
Contour LevelBy AUTHOR: 0.0328 / Movie #1: 0.0328
Minimum - Maximum-0.07270714 - 0.16208321
Average (Standard dev.)0.0001006831 (±0.0023274135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 544.752 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7461.7461.746
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z544.752544.752544.752
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.0730.1620.000

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Supplemental data

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Additional map: Phenix Resolve Cryo EM tool was used on...

Fileemd_11910_additional_1.map
AnnotationPhenix Resolve Cryo EM tool was used on the Relion 3D refined map and half maps to generate a density modified map. This map showed significant improvement in the H3 tail.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EM map of EZH2 on nucleosome obtained from signal particle subtra...

EntireName: EM map of EZH2 on nucleosome obtained from signal particle subtraction and focused refinement on PHF1-PRC2:dinucleosome map.
Components
  • Complex: EM map of EZH2 on nucleosome obtained from signal particle subtraction and focused refinement on PHF1-PRC2:dinucleosome map.
    • Complex: SUZ12 and EZH2
      • Protein or peptide: Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2
      • Protein or peptide: Polycomb protein SUZ12
    • Complex: Histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • DNA: Widom601 DNA plus linker
      • DNA: Widom601 DNA plus linker
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: EM map of EZH2 on nucleosome obtained from signal particle subtra...

SupramoleculeName: EM map of EZH2 on nucleosome obtained from signal particle subtraction and focused refinement on PHF1-PRC2:dinucleosome map.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: SUZ12 and EZH2

SupramoleculeName: SUZ12 and EZH2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histones

SupramoleculeName: Histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of...

MacromoleculeName: Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase ...Name: Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of Histone-lysine N-methyltransferase EZH2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine27 N-trimethyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.195328 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 PKCNYSFHAT PNTYKRKNTE TAL DNKPCG PQCYQHLEGA KEFAAALTAE RIKTPPKRPG GRRRGRLPNN SSRPSTPTIN VLESKDTDSD REAGTETGGE NNDK EEEEK KDETSSSSEA NSRCQTPIKM KPNIEPPENV EWSGAEASMF RVLIGTYYDN FCAIARLIGT KTCRQVYEFR VKESS IIAP APAEDVD(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) TPPR KKKRK HRLWAAHCRK IQLKKDGSSN HVYNYQPCDH PRQPCDSSCP CVIAQNFCEK FCQCSSECQN RFPGCRCKAQ CNTKQ CPCY LAVRECDPDL CLTCGAADHW DSKNVSCKNC SIQRGSKKHL LLAPSDVAGW GIFIKDPVQK NEFISEYCGE IISQDE ADR RGKVYDKYMC SFLFNLNNDF VVDATRKGNK IRFANHSVNP NCYAKVMMVN GDHRIGIFAK RAIQTGEELF FDYRYSQ AD ALKYVGIERE MEIP

UniProtKB: Histone-lysine N-methyltransferase EZH2, Histone-lysine N-methyltransferase EZH2

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Macromolecule #2: Polycomb protein SUZ12

MacromoleculeName: Polycomb protein SUZ12 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.181922 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #5: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #6: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Widom601 DNA plus linker

MacromoleculeName: Widom601 DNA plus linker / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.904535 KDa
SequenceString: (DT)(DC)(DA)(DT)(DA)(DC)(DT)(DG)(DG)(DA) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT) (DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG) (DT) (DC)(DG)(DT)(DA)(DG)(DA) ...String:
(DT)(DC)(DA)(DT)(DA)(DC)(DT)(DG)(DG)(DA) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT) (DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG) (DT) (DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC) (DC)(DG) (DC)(DT)(DT)(DA)(DA)(DA)(DC) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC) (DG)(DC)(DT) (DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA) (DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT) (DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT) (DA)(DT)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG) (DT)(DA)(DT)

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Macromolecule #8: Widom601 DNA plus linker

MacromoleculeName: Widom601 DNA plus linker / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.402852 KDa
SequenceString: (DA)(DT)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA) (DG)(DG)(DG)(DA)(DG)(DT) ...String:
(DA)(DT)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA) (DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC) (DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA)(DC) (DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA) (DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC)(DG) (DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG) (DG)(DG)(DA) (DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DT)(DA) (DT)(DG)(DA)

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Macromolecule #9: ZINC ION

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

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Macromolecule #10: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 10 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5hyn


Details: Other PDBs: 6T9L and 1AOI
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45849
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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