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- EMDB-4763: Cryo-EM structure of NCP_THF2(-1)-UV-DDB -

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Basic information

Entry
Database: EMDB / ID: EMD-4763
TitleCryo-EM structure of NCP_THF2(-1)-UV-DDB
Map data
Sample
  • Complex: UV-DDB bound to a THF2 containing nucleosome
    • Complex: Histone H3.1, Histone H2A, Histone H2BHistone H3
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
    • Complex: Histone H4
      • Protein or peptide: Histone H4
    • Complex: DNA
      • DNA: Human alpha-satellite DNA (145-MER)
      • DNA: Human alpha-satellite DNA (145-MER) with abasic sites at positions 97-98
    • Complex: DNA damage-binding protein 1(2), DNA damage-binding protein 2
      • Protein or peptide: DNA damage-binding protein 1
      • Protein or peptide: DNA damage-binding protein 2
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / Cul4A-RING E3 ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / Cul4A-RING E3 ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / site of DNA damage / viral release from host cell / negative regulation of tumor necrosis factor-mediated signaling pathway / pyrimidine dimer repair / ectopic germ cell programmed cell death / positive regulation of viral genome replication / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / protein autoubiquitination / CENP-A containing nucleosome / Packaging Of Telomere Ends / response to UV / epigenetic regulation of gene expression / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of gluconeogenesis / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / HDACs deacetylate histones / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / DNA Damage Recognition in GG-NER / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Dual Incision in GG-NER / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / HDMs demethylate histones / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / DNA Damage/Telomere Stress Induced Senescence / Formation of TC-NER Pre-Incision Complex / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Dual incision in TC-NER / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Gap-filling DNA repair synthesis and ligation in TC-NER / HCMV Early Events / protein polyubiquitination / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / positive regulation of protein catabolic process / cellular response to UV / UCH proteinases / rhythmic process / nucleosome / protein-macromolecule adaptor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / gene expression / cell junction / site of double-strand break / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
Similarity search - Function
DNA damage-binding protein 2 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...DNA damage-binding protein 2 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / 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 / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / DNA damage-binding protein 1 / DNA damage-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMatsumoto S / Cavadini S / Bunker RD / Thoma NH
Funding support Switzerland, Japan, 7 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII3_160734/1 Switzerland
European Commission667951
European Union666068
Japan Society for the Promotion of ScienceJP18H05534 Japan
European Commission705354
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of ScienceJP16H06307 Japan
CitationJournal: Nature / Year: 2019
Title: DNA damage detection in nucleosomes involves DNA register shifting.
Authors: Syota Matsumoto / Simone Cavadini / Richard D Bunker / Ralph S Grand / Alessandro Potenza / Julius Rabl / Junpei Yamamoto / Andreas D Schenk / Dirk Schübeler / Shigenori Iwai / Kaoru ...Authors: Syota Matsumoto / Simone Cavadini / Richard D Bunker / Ralph S Grand / Alessandro Potenza / Julius Rabl / Junpei Yamamoto / Andreas D Schenk / Dirk Schübeler / Shigenori Iwai / Kaoru Sugasawa / Hitoshi Kurumizaka / Nicolas H Thomä /
Abstract: Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced ...Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer or a DNA-damage mimic in various positions. We find that UV-DDB binds UV-damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA.
History
DepositionApr 2, 2019-
Header (metadata) releaseMay 22, 2019-
Map releaseJun 12, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r8z
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4763.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-16.73861 - 47.03089
Average (Standard dev.)0.00000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z308.000308.000308.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-16.73947.0310.000

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Supplemental data

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Sample components

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Entire : UV-DDB bound to a THF2 containing nucleosome

EntireName: UV-DDB bound to a THF2 containing nucleosome
Components
  • Complex: UV-DDB bound to a THF2 containing nucleosome
    • Complex: Histone H3.1, Histone H2A, Histone H2BHistone H3
      • Protein or peptide: Histone H3.1Histone H3
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
    • Complex: Histone H4
      • Protein or peptide: Histone H4
    • Complex: DNA
      • DNA: Human alpha-satellite DNA (145-MER)
      • DNA: Human alpha-satellite DNA (145-MER) with abasic sites at positions 97-98
    • Complex: DNA damage-binding protein 1(2), DNA damage-binding protein 2
      • Protein or peptide: DNA damage-binding protein 1
      • Protein or peptide: DNA damage-binding protein 2

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Supramolecule #1: UV-DDB bound to a THF2 containing nucleosome

SupramoleculeName: UV-DDB bound to a THF2 containing nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 199 KDa

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Supramolecule #2: Histone H3.1, Histone H2A, Histone H2B

SupramoleculeName: Histone H3.1, Histone H2A, Histone H2B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #3: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #5: DNA damage-binding protein 1(2), DNA damage-binding protein 2

SupramoleculeName: DNA damage-binding protein 1(2), DNA damage-binding protein 2
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

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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: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

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Macromolecule #7: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.766305 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KVDENLYFQG GGRMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMEL FRPKGESKDL LFILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY D GLFKVIPL ...String:
MASWSHPQFE KVDENLYFQG GGRMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMEL FRPKGESKDL LFILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY D GLFKVIPL DRDNKELKAF NIRLEELHVI DVKFLYGCQA PTICFVYQDP QGRHVKTYEV SLREKEFNKG PWKQENVEAE AS MVIAVPE PFGGAIIIGQ ESITYHNGDK YLAIAPPIIK QSTIVCHNRV DPNGSRYLLG DMEGRLFMLL LEKEEQMDGT VTL KDLRVE LLGETSIAEC LTYLDNGVVF VGSRLGDSQL VKLNVDSNEQ GSYVVAMETF TNLGPIVDMC VVDLERQGQG QLVT CSGAF KEGSLRIIRN GIGIHEHASI DLPGIKGLWP LRSDPNRETD DTLVLSFVGQ TRVLMLNGEE VEETELMGFV DDQQT FFCG NVAHQQLIQI TSASVRLVSQ EPKALVSEWK EPQAKNISVA SCNSSQVVVA VGRALYYLQI HPQELRQISH TEMEHE VAC LDITPLGDSN GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH YLLCALGDGA LFYFGLN IE TGLLSDRKKV TLGTQPTVLR TFRSLSTTNV FACSDRPTVI YSSNHKLVFS NVNLKEVNYM CPLNSDGYPD SLALANNS T LTIGTIDEIQ KLHIRTVPLY ESPRKICYQE VSQCFGVLSS RIEVQDTSGG TTALRPSAST QALSSSVSSS KLFSSSTAP HETSFGEEVE VHNLLIIDQH TFEVLHAHQF LQNEYALSLV SCKLGKDPNT YFIVGTAMVY PEEAEPKQGR IVVFQYSDGK LQTVAEKEV KGAVYSMVEF NGKLLASINS TVRLYEWTTE KELRTECNHY NNIMALYLKT KGDFILVGDL MRSVLLLAYK P MEGNFEEI ARDFNPNWMS AVEILDDDNF LGAENAFNLF VCQKDSAATT DEERQHLQEV GLFHLGEFVN VFCHGSLVMQ NL GETSTPT QGSVLFGTVN GMIGLVTSLS ESWYNLLLDM QNRLNKVIKS VGKIEHSFWR SFHTERKTEP ATGFIDGDLI ESF LDISRP KMQEVVANLQ YDDGSGMKRE ATADDLIKVV EELTRIH

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Macromolecule #8: DNA damage-binding protein 2

MacromoleculeName: DNA damage-binding protein 2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.261277 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGGRMAPKKR PETQKTSEIV LRPRNKRSRS PLELEPEAKK LCAKGSGPSR RCDSDCLWVG LAGPQILPPC RSIVRTLHQH KLGRASWPS VQQGLQQSFL HTLDSYRILQ KAAPFDRRAT SLAWHPTHPS TVAVGSKGGD IMLWNFGIKD KPTFIKGIGA G GSITGLKF ...String:
GGGRMAPKKR PETQKTSEIV LRPRNKRSRS PLELEPEAKK LCAKGSGPSR RCDSDCLWVG LAGPQILPPC RSIVRTLHQH KLGRASWPS VQQGLQQSFL HTLDSYRILQ KAAPFDRRAT SLAWHPTHPS TVAVGSKGGD IMLWNFGIKD KPTFIKGIGA G GSITGLKF NPLNTNQFYA SSMEGTTRLQ DFKGNILRVF ASSDTINIWF CSLDVSASSR MVVTGDNVGN VILLNMDGKE LW NLRMHKK KVTHVALNPC CDWFLATASV DQTVKIWDLR QVRGKASFLY SLPHRHPVNA ACFSPDGARL LTTDQKSEIR VYS ASQWDC PLGLIPHPHR HFQHLTPIKA AWHPRYNLIV VGRYPDPNFK SCTPYELRTI DVFDGNSGKM MCQLYDPESS GISS LNEFN PMGDTLASAM GYHILIWSQE EARTRK

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Macromolecule #5: Human alpha-satellite DNA (145-MER)

MacromoleculeName: Human alpha-satellite DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.756648 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DT)(DT)(DC)(DA)(DG) (DC)(DT)(DG) (DA)(DA)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG) (DG)(DA)(DG)(DC) (DA)(DG)(DT)(DT)(DT) (DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC) (DT)(DT)(DT)(DT)(DG) (DG)(DT)(DA)(DG) (DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DT)(DG)(DG)(DA)(DT)(DA) (DT)(DT)(DG) (DA)(DT)

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Macromolecule #6: Human alpha-satellite DNA (145-MER) with abasic sites at position...

MacromoleculeName: Human alpha-satellite DNA (145-MER) with abasic sites at positions 97-98
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.461449 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG) (DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG) (DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA) (DG)(DC)(DT)(DG)(DA)(DA)(DC)(DC)(DA)(DG) (DC)(DT)(DG) (DA)(DA)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(3DR)(3DR) (DG)(DA)(DG) (DC)(DA)(DG)(DT)(DT)(DT) (DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC) (DT)(DT)(DT)(DT) (DG)(DG)(DT)(DA)(DG) (DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DT)(DG)(DG)(DA)(DT) (DA)(DT)(DT)(DG) (DA)(DT)

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chlorideSodium chloride
50.0 mMHEPES
0.25 mMTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.0 mm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 129986

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Atomic model buiding 1

Initial model
PDB IDChain

chain_id: I

chain_id: J

chain_id: A

chain_id: B

chain_id: C

chain_id: D

chain_id: E

chain_id: F

chain_id: G

chain_id: H

chain_id: B

chain_id: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6r8z:
Cryo-EM structure of NCP_THF2(-1)-UV-DDB

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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

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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

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