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- EMDB-18778: Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-18778
TitleStructure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Map datacanonical DNMT3A1-DNMt3L-NCP H2AK119ub map
Sample
  • Complex: DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA
    • Complex: H2AKc119ub Nucleosome wrapped with 195 bp Widom601 DNA
      • Protein or peptide: Histone H3 (Fragment)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • DNA: DNA (145-MER)
      • DNA: DNA (145-MER)
    • Complex: DNMT3A1-DNMT3L complex
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
    • Complex: Ubiquitin
KeywordsChromatin / Nucleosome / methyltransferase / Ubiquitin / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / DNA (cytosine-5-)-methyltransferase activity / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase ...positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / DNA (cytosine-5-)-methyltransferase activity / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / autosome genomic imprinting / SUMOylation of DNA methylation proteins / XY body / cellular response to ethanol / response to vitamin A / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / hepatocyte apoptotic process / chromosome, centromeric region / catalytic complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Transferases; Transferring one-carbon groups; Methyltransferases / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / post-embryonic development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to amino acid stimulus / Transcriptional regulation by small RNAs / response to cocaine / Formation of the beta-catenin:TCF transactivating complex / response to lead ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / Transcriptional regulation of granulopoiesis / response to toxic substance / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / neuron differentiation / transcription corepressor activity / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / spermatogenesis / methylation
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / 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 / 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 H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H3 / Histone H2A type 1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWapenaar H / Wilson MD
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust210493/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)T029471/1 United Kingdom
CitationJournal: EMBO Rep / Year: 2024
Title: The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.
Authors: Hannah Wapenaar / Gillian Clifford / Willow Rolls / Moira Pasquier / Hayden Burdett / Yujie Zhang / Gauri Deák / Juan Zou / Christos Spanos / Mark R D Taylor / Jacquie Mills / James A ...Authors: Hannah Wapenaar / Gillian Clifford / Willow Rolls / Moira Pasquier / Hayden Burdett / Yujie Zhang / Gauri Deák / Juan Zou / Christos Spanos / Mark R D Taylor / Jacquie Mills / James A Watson / Dhananjay Kumar / Richard Clark / Alakta Das / Devisree Valsakumar / Janice Bramham / Philipp Voigt / Duncan Sproul / Marcus D Wilson /
Abstract: DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of ...DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs.
History
DepositionOct 27, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18778.png

Downloads & links

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Map

FileDownload / File: emd_18778.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcanonical DNMT3A1-DNMt3L-NCP H2AK119ub map
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.336 Å		0.83 Å/pix.
x 384 pix.
= 318.336 Å		0.83 Å/pix.
x 384 pix.
= 318.336 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
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Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.36610663 - 0.8900524
Average (Standard dev.)0.0004845655 (±0.023594815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18778_msk_1.map
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Additional map: DNMT3A1-DNMt3L-NCP H2AK119ub processed in relion with circular mask...

Fileemd_18778_additional_1.map
AnnotationDNMT3A1-DNMt3L-NCP H2AK119ub processed in relion with circular mask and offset applied
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Additional map: canonical DNMT3A1-DNMt3L-NCP H2AK119ub map sharpened with bfactor -50

Fileemd_18778_additional_2.map
Annotationcanonical DNMT3A1-DNMt3L-NCP H2AK119ub map sharpened with bfactor -50
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Additional map: DNMT3A1-DNMt3L-NCP H2AK119ub processed by homogenous refinement with wider...

Fileemd_18778_additional_3.map
AnnotationDNMT3A1-DNMt3L-NCP H2AK119ub processed by homogenous refinement with wider mask (map 2)
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Additional map: DNMT3A1-DNMt3L-NCP H2AK119ub processed by homogenous refinement with wider...

Fileemd_18778_additional_4.map
AnnotationDNMT3A1-DNMt3L-NCP H2AK119ub processed by homogenous refinement with wider mask (map 2)
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Half map: canonical DNMT3A1-DNMt3L-NCP H2AK119ub halfmap 1

Fileemd_18778_half_map_1.map
Annotationcanonical DNMT3A1-DNMt3L-NCP H2AK119ub halfmap 1
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Half map: canonical DNMT3A1-DNMt3L-NCP H2AK119ub halfmap 2

Fileemd_18778_half_map_2.map
Annotationcanonical DNMT3A1-DNMt3L-NCP H2AK119ub halfmap 2
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Sample components

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Entire : DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrap...

EntireName: DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA
Components
  • Complex: DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA
    • Complex: H2AKc119ub Nucleosome wrapped with 195 bp Widom601 DNA
      • Protein or peptide: Histone H3 (Fragment)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • DNA: DNA (145-MER)
      • DNA: DNA (145-MER)
    • Complex: DNMT3A1-DNMT3L complex
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
    • Complex: Ubiquitin

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Supramolecule #1: DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrap...

SupramoleculeName: DNMT3A1-DNMT3L in complex with a human H2AKc119ub nucleosome wrapped with 195bp of Widom-601 positioning DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 147 KDa

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Supramolecule #2: H2AKc119ub Nucleosome wrapped with 195 bp Widom601 DNA

SupramoleculeName: H2AKc119ub Nucleosome wrapped with 195 bp Widom601 DNA
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNMT3A1-DNMT3L complex

SupramoleculeName: DNMT3A1-DNMT3L complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3 (Fragment)

MacromoleculeName: Histone H3 (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.257838 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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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: Homo sapiens (human)
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 #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3
Details: H2A crosslinked at K119C with acetone linker to ubiquitin G76C
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.964305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKC TESHHKAKGK

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 7 / Details: copurified with DNMT3L / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.269734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMPAMPSS GPGDTSSSAA EREEDRKDGE EQEEPRGKEE RQEPSTTARK VGRPGRKRKH PPVESGDTPK DPAVISKSPS MAQDSGASE LLPNGDLEKR SEPQPEEGSP AGGQKGGAPA EGEGAAETLP EASRAVENGC CTPKEGRGAP AEAGKEQKET N IESMKMEG ...String:
SNAMPAMPSS GPGDTSSSAA EREEDRKDGE EQEEPRGKEE RQEPSTTARK VGRPGRKRKH PPVESGDTPK DPAVISKSPS MAQDSGASE LLPNGDLEKR SEPQPEEGSP AGGQKGGAPA EGEGAAETLP EASRAVENGC CTPKEGRGAP AEAGKEQKET N IESMKMEG SRGRLRGGLG WESSLRQRPM PRLTFQAGDP YYISKRKRDE WLARWKREAE KKAKVIAGMN AVEENQGPGE SQ KVEEASP PAVQQPTDPA SPTVATTPEP VGSDAGDKNA TKAGDDEPEY EDGRGFGIGE LVWGKLRGFS WWPGRIVSWW MTG RSRAAE GTRWVMWFGD GKFSVVCVEK LMPLSSFCSA FHQATYNKQP MYRKAIYEVL QVASSRAGKL FPVCHDSDES DTAK AVEVQ NKPMIEWALG GFQPSGPKGL EPPEEEKNPY KEVYTDMWVE PEAAAYAPPP PAKKPRKSTA EKPKVKEIID ERTRE RLVY EVRQKCRNIE DICISCGSLN VTLEHPLFVG GMCQNCKNCF LECAYQYDDD GYQSYCTICC GGREVLMCGN NNCCRC FCV ECVDLLVGPG AAQAAIKEDP WNCYMCGHKG TYGLLRRRED WPSRLQMFFA NNHDQEFDPP KVYPPVPAEK RKPIRVL SL FDGIATGLLV LKDLGIQVDR YIASEVCEDS ITVGMVRHQG KIMYVGDVRS VTQKHIQEWG PFDLVIGGSP CNDLSIVN P ARKGLYEGTG RLFFEFYRLL HDARPKEGDD RPFFWLFENV VAMGVSDKRD ISRFLESNPV MIDAKEVSAA HRARYFWGN LPGMNRPLAS TVNDKLELQE CLEHGRIAKF SKVRTITTRS NSIKQGKDQH FPVFMNEKED ILWCTEMERV FGFPVHYTDV SNMSRLARQ RLLGRSWSVP VIRHLFAPLK EYFACV

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

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Macromolecule #5: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 60.64259 KDa
SequenceString: (DG)(DG)(DT)(DG)(DG)(DG)(DC)(DG)(DC)(DG) (DC)(DG)(DA)(DA)(DC)(DT)(DG)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DG)(DC)(DC) (DT)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DG) (DG) (DC)(DG)(DT)(DA)(DT)(DG) ...String:
(DG)(DG)(DT)(DG)(DG)(DG)(DC)(DG)(DC)(DG) (DC)(DG)(DA)(DA)(DC)(DT)(DG)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DG)(DC)(DC) (DT)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DG) (DG) (DC)(DG)(DT)(DA)(DT)(DG)(DG)(DT) (DG)(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)

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Macromolecule #6: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.771035 KDa
SequenceString: (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) ...String:
(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)(DC)(DA)(DC)(DC)(DA)(DT)(DA) (DC)(DG)(DC)(DC)(DC)(DT)(DA) (DA)(DT) (DT)(DA)(DG)(DA)(DG)(DG)(DC)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DC)(DA) (DG) (DT)(DT)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DC) (DC)(DA)(DC)(DC)

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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

Concentration0.13 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
15.0 mMC8H18N2O4SHEPES
65.0 mMNaClsodium chloride
1.0 mMC4H10O2S2Dithiothreitol
0.1 mMC15H22N6O5SS-Adenosyl methionine

Details: 15 mM HEPES pH 7.5, 65 mM NaCl, 1 mM DTT, 0.1 mM S-Adenosyl methionine
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 15491 / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7826521
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 191397
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 191397 / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
chain_id: K, source_name: Other, initial_model_type: in silico modelModel Angelo
source_name: PDB, initial_model_type: experimental model

7xd1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 50
Output model

PDB-8qzm:
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome

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