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- EMDB-4762: Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB -

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Basic information

Entry
Database: EMDB / ID: EMD-4762
TitleCryo-EM structure of NCP-6-4PP(-1)-UV-DDB
Map data
Sample
  • Complex: UV-DDB bound to a 6-4PP containing nucleosome
    • Complex: histones
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA damage-binding proteins
      • Protein or peptide: DNA damage-binding protein 1
      • Protein or peptide: DNA damage-binding protein 2
    • Complex: DNA
      • DNA: Human alpha-satellite DNA (145-MER)
      • DNA: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96
    • Complex: histones
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H4
KeywordsDNA damage / Nucleosome / 6-4 photoproduct / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / 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 / viral release from host cell / site of DNA damage / pyrimidine dimer repair / negative regulation of tumor necrosis factor-mediated signaling pathway / ectopic germ cell programmed cell death / positive regulation of viral genome replication / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / response to UV / proteasomal protein catabolic process / protein autoubiquitination / Chromatin modifying enzymes / 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 / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / nucleotide-excision repair / HDACs deacetylate histones / TP53 Regulates Transcription of DNA Repair Genes / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Recognition of DNA damage by PCNA-containing replication complex / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Dual Incision in GG-NER / Meiotic recombination / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Pre-NOTCH Transcription and Translation / Formation of TC-NER Pre-Incision Complex / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / protein polyubiquitination / Dual incision in TC-NER / HCMV Early Events / Gap-filling DNA repair synthesis and ligation in TC-NER / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of protein catabolic process / cellular response to UV / structural constituent of chromatin / UCH proteinases / cell junction / antibacterial humoral response / rhythmic process / nucleosome / heterochromatin formation / nucleosome assembly
Similarity search - Function
DNA damage-binding protein 2 / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / Histone H2B signature. / Histone H2A conserved site ...DNA damage-binding protein 2 / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 domain / Histone-fold / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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: 4.3 Å
AuthorsMatsumoto S / Cavadini S
Funding support Switzerland, Japan, 7 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII3_160734/1 Switzerland
European Union666068
European Commission667951
European Commission705354
Japan Society for the Promotion of ScienceJP18H05534 Japan
Japan Society for the Promotion of ScienceJP16H06307 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101076 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-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6r8y
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4762.png

Downloads & links

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Map

FileDownload / File: emd_4762.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-14.282897999999999 - 32.150463000000002
Average (Standard dev.)0.00045621197 (±0.9515588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-14.28332.1500.000

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Supplemental data

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Sample components

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Entire : UV-DDB bound to a 6-4PP containing nucleosome

EntireName: UV-DDB bound to a 6-4PP containing nucleosome
Components
  • Complex: UV-DDB bound to a 6-4PP containing nucleosome
    • Complex: histones
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
    • Complex: DNA damage-binding proteins
      • Protein or peptide: DNA damage-binding protein 1
      • Protein or peptide: DNA damage-binding protein 2
    • Complex: DNA
      • DNA: Human alpha-satellite DNA (145-MER)
      • DNA: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96
    • Complex: histones
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H4

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Supramolecule #1: UV-DDB bound to a 6-4PP containing nucleosome

SupramoleculeName: UV-DDB bound to a 6-4PP containing nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightTheoretical: 199 KDa

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Supramolecule #2: histones

SupramoleculeName: histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA damage-binding proteins

SupramoleculeName: DNA damage-binding proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: histones

SupramoleculeName: histones / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2, #5
Source (natural)Organism: Homo sapiens (human)

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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

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

UniProtKB: Histone H4

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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

UniProtKB: Histone H2A type 1-B/E

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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

UniProtKB: Histone H2B type 1-J

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #8: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.425812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVMEL FRPKGESKDL LFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL YDGLFKVIPL DRDNKELKAF N IRLEELHV ...String:
GGGRMSYNYV VTAQKPTAVN GCVTGHFTSA EDLNLLIAKN TRLEIYVVTA EGLRPVKEVG MYGKIAVMEL FRPKGESKDL LFILTAKYN ACILEYKQSG ESIDIITRAH GNVQDRIGRP SETGIIGIID PECRMIGLRL YDGLFKVIPL DRDNKELKAF N IRLEELHV IDVKFLYGCQ APTICFVYQD PQGRHVKTYE VSLREKEFNK GPWKQENVEA EASMVIAVPE PFGGAIIIGQ ES ITYHNGD KYLAIAPPII KQSTIVCHNR VDPNGSRYLL GDMEGRLFML LLEKEEQMDG TVTLKDLRVE LLGETSIAEC LTY LDNGVV FVGSRLGDSQ LVKLNVDSNE QGSYVVAMET FTNLGPIVDM CVVDLERQGQ GQLVTCSGAF KEGSLRIIRN GIGI HEHAS IDLPGIKGLW PLRSDPNRET DDTLVLSFVG QTRVLMLNGE EVEETELMGF VDDQQTFFCG NVAHQQLIQI TSASV RLVS QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDITPLGDSN GLSPLC AIG LWTDISARIL KLPSFELLHK EMLGGEIIPR SILMTTFESS HYLLCALGDG ALFYFGLNIE TGLLSDRKKV TLGTQPT VL RTFRSLSTTN VFACSDRPTV IYSSNHKLVF SNVNLKEVNY MCPLNSDGYP DSLALANNST LTIGTIDEIQ KLHIRTVP L YESPRKICYQ EVSQCFGVLS SRIEVQDTSG GTTALRPSAS TQALSSSVSS SKLFSSSTAP HETSFGEEVE VHNLLIIDQ HTFEVLHAHQ FLQNEYALSL VSCKLGKDPN TYFIVGTAMV YPEEAEPKQG RIVVFQYSDG KLQTVAEKEV KGAVYSMVEF NGKLLASIN STVRLYEWTT EKELRTECNH YNNIMALYLK TKGDFILVGD LMRSVLLLAY KPMEGNFEEI ARDFNPNWMS A VEILDDDN FLGAENAFNL FVCQKDSAAT TDEERQHLQE VGLFHLGEFV NVFCHGSLVM QNLGETSTPT QGSVLFGTVN GM IGLVTSL SESWYNLLLD MQNRLNKVIK SVGKIEHSFW RSFHTERKTE PATGFIDGDL IESFLDISRP KMQEVVANLQ YDD GSGMKR EATADDLIKV VEELTRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #9: DNA damage-binding protein 2

MacromoleculeName: DNA damage-binding protein 2 / type: protein_or_peptide / ID: 9 / 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

UniProtKB: DNA damage-binding protein 2

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Macromolecule #6: Human alpha-satellite DNA (145-MER)

MacromoleculeName: Human alpha-satellite DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.780672 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)(DA)(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 #7: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96

MacromoleculeName: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96
type: dna / ID: 7
Details: 145 bp human alpha-satellite with a 6-4 pyrimidine-pyrimidone (6-4PP) at base positions 95-96
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.709645 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)(T64)(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 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
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 6.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 84000
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION

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Atomic model buiding 1

Initial model
PDB IDChain

4zux

chain_id: I, source_name: PDB, initial_model_type: experimental model

4zux

chain_id: J, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: A, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: B, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: C, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: D, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: E, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: F, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: G, source_name: PDB, initial_model_type: experimental model

5y0c

chain_id: H, source_name: PDB, initial_model_type: experimental model

4e54

chain_id: B, source_name: PDB, initial_model_type: experimental model

3ei4

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6r8y:
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB

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