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- EMDB-20281: The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20281
TitleThe cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.
Map dataThe cryo-EM map of human DNMT3A2/3B3 with NCP.
Sample
  • Complex: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
    • Complex: Histone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA (167-MER)
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
    • Complex: DNA (cytosine-5)-methyltransferase
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3B
  • Ligand: CHLORIDE ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
Keywordsmethyltransferase / complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / cellular response to bisphenol A / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting ...positive regulation of cellular response to hypoxia / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / cellular response to bisphenol A / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / XY body / response to vitamin A / cellular response to ethanol / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / catalytic complex / chromosome, centromeric region / heterochromatin / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cellular response to amino acid stimulus / response to lead ion / NoRC negatively regulates rRNA expression / euchromatin / neuron differentiation / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / response to estradiol / cellular response to hypoxia / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / methylation / response to xenobiotic stimulus / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / DNA (cytosine-5-)-methyltransferase, N-terminal / DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site ...DNA (cytosine-5)-methyltransferase 3A, ADD domain / DNA (cytosine-5-)-methyltransferase, N-terminal / DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsXu TH / Liu M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: Nature / Year: 2020
Title: Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.
Authors: Ting-Hai Xu / Minmin Liu / X Edward Zhou / Gangning Liang / Gongpu Zhao / H Eric Xu / Karsten Melcher / Peter A Jones /
Abstract: CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially ...CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core, and they favour the methylation of linker DNA at positioned nucleosomes. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.
History
DepositionJun 11, 2019-
Header (metadata) releaseJun 26, 2019-
Map releaseJun 17, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pa7
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20281.png

Downloads & links

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Map

FileDownload / File: emd_20281.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM map of human DNMT3A2/3B3 with NCP.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 360 pix.
= 370.44 Å		1.03 Å/pix.
x 360 pix.
= 370.44 Å		1.03 Å/pix.
x 360 pix.
= 370.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.042697918 - 0.093867235
Average (Standard dev.)0.00013697847 (±0.0018605059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 370.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z370.440370.440370.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0430.0940.000

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Supplemental data

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Sample components

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Entire : A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes

EntireName: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
Components
  • Complex: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
    • Complex: Histone
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: DNA (167-MER)
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
    • Complex: DNA (cytosine-5)-methyltransferase
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3B
  • Ligand: CHLORIDE ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes

SupramoleculeName: A ternary complex of DNMT3A/B asymmetrically binds to the nucleosomes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 520 KDa

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Supramolecule #2: Histone

SupramoleculeName: Histone / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: DNA (167-MER)

SupramoleculeName: DNA (167-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: DNA (cytosine-5)-methyltransferase

SupramoleculeName: DNA (cytosine-5)-methyltransferase / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / 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 #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / 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 type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: DNA (cytosine-5)-methyltransferase 3A

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.914711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNAVEENQGP GESQKVEEAS PPAVQQPTDP ASPTVATTPE PVGSDAGDKN ATKAGDDEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVS WWMTGRSRAA EGTRWVMWFG DGKFSVVCVE KLMPLSSFCS AFHQATYNKQ PMYRKAIYEV LQVASSRAGK L FPVCHDSD ...String:
MNAVEENQGP GESQKVEEAS PPAVQQPTDP ASPTVATTPE PVGSDAGDKN ATKAGDDEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVS WWMTGRSRAA EGTRWVMWFG DGKFSVVCVE KLMPLSSFCS AFHQATYNKQ PMYRKAIYEV LQVASSRAGK L FPVCHDSD ESDTAKAVEV QNKPMIEWAL GGFQPSGPKG LEPPEEEKNP YKEVYTDMWV EPEAAAYAPP PPAKKPRKST AE KPKVKEI IDERTRERLV YEVRQKCRNI EDICISCGSL NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC CGG REVLMC GNNNCCRCFC VECVDLLVGP GAAQAAIKED PWNCYMCGHK GTYGLLRRRE DWPSRLQMFF ANNHDQEFDP PKVY PPVPA EKRKPIRVLS LFDGIATGLL VLKDLGIQVD RYIASEVCED SITVGMVRHQ GKIMYVGDVR SVTQKHIQEW GPFDL VIGG SPCNDLSIVN PARKGLYEGT GRLFFEFYRL LHDARPKEGD DRPFFWLFEN VVAMGVSDKR DISRFLESNP VMIDAK EVS AAHRARYFWG NLPGMNRPLA STVNDKLELQ ECLEHGRIAK FSKVRTITTR SNSIKQGKDQ HFPVFMNEKE DILWCTE ME RVFGFPVHYT DVSNMSRLAR QRLLGRSWSV PVIRHLFAPL KEYFACV

UniProtKB: DNA (cytosine-5)-methyltransferase 3A

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Macromolecule #8: DNA (cytosine-5)-methyltransferase 3B

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3B / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.294945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR SSSRLSKREV SSLLSYTQDL TGDGDGEDGD GSDTPVMPK LFRETRTRSE SPAVRTRNNN SVSSRERHRP SPRSTRGRQG RNHVDESPVE FPATRSLRRR ATASAGTPWP S PPSSYLTI ...String:
MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR SSSRLSKREV SSLLSYTQDL TGDGDGEDGD GSDTPVMPK LFRETRTRSE SPAVRTRNNN SVSSRERHRP SPRSTRGRQG RNHVDESPVE FPATRSLRRR ATASAGTPWP S PPSSYLTI DLTDDTEDTH GTPQSSSTPY ARLAQDSQQG GMESPQVEAD SGDGDSSEYQ DGKEFGIGDL VWGKIKGFSW WP AMVVSWK ATSKRQAMSG MRWVQWFGDG KFSEVSADKL VALGLFSQHF NLATFNKLVS YRKAMYHALE KARVRAGKTF PSS PGDSLE DQLKPMLEWA HGGFKPTGIE GLKPNNTQPE NKTRRRTADD SATSDYCPAP KRLKTNCYNN GKDRGDEDQS REQM ASDVA NNKSSLEDGC LSCGRKNPVS FHPLFEGGLC QTCRDRFLEL FYMYDDDGYQ SYCTVCCEGR ELLLCSNTSC CRCFC VECL EVLVGTGTAA EAKLQEPWSC YMCLPQRCHG VLRRRKDWNV RLQAFFTSDT GLEYEAPKLY PAIPAARRRP IRVLSL FDG IATGYLVLKE LGIKVGKYVA SEVCEESIAV GTVKHEGNIK YVNDVRNITK KNIEEWGPFD LVIGGSPCND LSNVNPA RK GLYEGTGRLF FEFYHLLNYS RPKEGDDRPF FWMFENVVAM KVGDKRDISR FLECNPVMID AIKVSAAHRA RYFWGNLP G MNRIFGFPVH YTDVSNMGRG ARQKLLGRSW SVPVIRHLFA PLKDYFACE

UniProtKB: DNA (cytosine-5)-methyltransferase 3B

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Macromolecule #5: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.327652 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (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) ...String:
(DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (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)(DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.785953 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(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) ...String:
(DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(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)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #9: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #10: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 10 / Number of copies: 2 / 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

Concentration0.2 mg/mL
BufferpH: 8
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.0 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2190114
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 599344
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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