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- EMDB-4764: Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A -

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Basic information

Entry
Database: EMDB / ID: EMD-4764
TitleCryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Map data
Sample
  • Complex: UV-DDB bound to a THF2 containing nucleosome class A
    • 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 93-94
    • 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


negative regulation of reproductive process / negative regulation of developmental process / positive regulation by virus of viral protein levels in host cell / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / biological process involved in interaction with symbiont ...negative regulation of reproductive process / negative regulation of developmental process / positive regulation by virus of viral protein levels in host cell / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / UV-damage excision repair / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / biological process involved in interaction with symbiont / histone H2A monoubiquitination / site of DNA damage / ectopic germ cell programmed cell death / cullin family protein binding / protein localization to CENP-A containing chromatin / negative regulation of megakaryocyte differentiation / positive regulation of gluconeogenesis / viral release from host cell / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Chromatin modifying enzymes / negative regulation of tumor necrosis factor-mediated signaling pathway / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / chromatin organization => GO:0006325 / protein autoubiquitination / pyrimidine dimer repair / 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 / response to UV / Interleukin-7 signaling / telomere organization / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / chromatin organization => GO:0006325 / DNA methylation / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / HDACs deacetylate histones / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / nuclear chromosome / Nonhomologous End-Joining (NHEJ) / proteasomal protein catabolic process / NoRC negatively regulates rRNA expression / DNA Damage Recognition in GG-NER / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / B-WICH complex positively regulates rRNA expression / lipopolysaccharide binding / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / G2/M DNA damage checkpoint / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Metalloprotease DUBs / DNA Damage/Telomere Stress Induced Senescence / Formation of Incision Complex in GG-NER / RMTs methylate histone arginines / positive regulation of protein catabolic process / regulation of circadian rhythm / HDMs demethylate histones / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nucleosome assembly / Meiotic recombination / Pre-NOTCH Transcription and Translation / PKMTs methylate histone lysines / HCMV Early Events / Wnt signaling pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / protein-macromolecule adaptor activity / Transcriptional regulation of granulopoiesis / protein polyubiquitination / UCH proteinases / nucleosome / cellular response to UV / DNA-templated transcription initiation / Neddylation / rhythmic process / site of double-strand break / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of viral genome replication / proteasome-mediated ubiquitin-dependent protein catabolic process
Similarity search - Function
DNA damage-binding protein 2 / DNA damage-binding protein 1 / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. ...DNA damage-binding protein 2 / DNA damage-binding protein 1 / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Histone H4 signature. / Histone H4, conserved site / 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 / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats 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: 4.5 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: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r90
  • Surface level: 3.5
  • 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_4764.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
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-9.876421 - 27.450775
Average (Standard dev.)-0.003245564 (±0.7673506)
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
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-9.87627.451-0.003

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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 class A

EntireName: UV-DDB bound to a THF2 containing nucleosome class A
Components
  • Complex: UV-DDB bound to a THF2 containing nucleosome class A
    • 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 93-94
    • 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 class A

SupramoleculeName: UV-DDB bound to a THF2 containing nucleosome class A / 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: 50.601844 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASWSHPQFE KVDENLYFQG GGRMAPKKRP ETQKTSEIVL RPRNKRSRSP LELEPEAKKL CAKGSGPSRR CDSDCLWVGL AGPQILPPC RSIVRTLHQH KLGRASWPSV QQGLQQSFLH TLDSYRILQK AAPFDRRATS LAWHPTHPST VAVGSKGGDI M LWNFGIKD ...String:
MASWSHPQFE KVDENLYFQG GGRMAPKKRP ETQKTSEIVL RPRNKRSRSP LELEPEAKKL CAKGSGPSRR CDSDCLWVGL AGPQILPPC RSIVRTLHQH KLGRASWPSV QQGLQQSFLH TLDSYRILQK AAPFDRRATS LAWHPTHPST VAVGSKGGDI M LWNFGIKD KPTFIKGIGA GGSITGLKFN PLNTNQFYAS SMEGTTRLQD FKGNILRVFA SSDTINIWFC SLDVSASSRM VV TGDNVGN VILLNMDGKE LWNLRMHKKK VTHVALNPCC DWFLATASVD QTVKIWDLRQ VRGKASFLYS LPHRHPVNAA CFS PDGARL LTTDQKSEIR VYSASQWDCP LGLIPHPHRH FQHLTPIKAA WHPRYNLIVV GRYPDPNFKS CTPYELRTID VFDG NSGKM MCQLYDPESS GISSLNEFNP MGDTLASAMG YHILIWSQEE ARTRK

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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 93-94
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.452434 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)(3DR)(3DR)(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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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 / Number grids imaged: 1 / Average exposure time: 6.0 sec. / 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 128763

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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
Output model

PDB-6r90:
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A

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