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

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ID or keywords:

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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 H2B
      • Protein or peptide: Histone H3.1
      • 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
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 / Cul4-RING E3 ubiquitin ligase complex / 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 / 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 / Cul4-RING E3 ubiquitin ligase complex / 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 / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / negative regulation of tumor necrosis factor-mediated signaling pathway / pyrimidine dimer repair / negative regulation of megakaryocyte differentiation / protein autoubiquitination / positive regulation of viral genome replication / proteasomal protein catabolic process / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / response to UV / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Recognition of DNA damage by PCNA-containing replication complex / Formation of the beta-catenin:TCF transactivating complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / DNA Damage/Telomere Stress Induced Senescence / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Wnt signaling pathway / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Formation of Incision Complex in GG-NER / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / Transcriptional regulation of granulopoiesis / positive regulation of protein catabolic process / structural constituent of chromatin / cellular response to UV / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / nucleosome / cell junction / nucleosome assembly
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 ...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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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: 4.5 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: 3.5
  • Imaged by UCSF Chimera
  • Download
  • 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

emd_4764.png

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-9.876421000000001 - 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 H2B
      • Protein or peptide: Histone H3.1
      • 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)

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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)

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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)

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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)

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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: 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

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 #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

UniProtKB: DNA damage-binding protein 1

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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

UniProtKB: DNA damage-binding protein 2

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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 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 128763
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
Output model

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

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
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