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- EMDB-22581: Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-22581
TitleCryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome
Map dataBRCA1-UbcH5c/BARD1 E3-E2 module bound to the nucleosome core particle
Sample
  • Complex: BRCA1-UbcH5c/BARD1 E3-E2 module bound to nucleosome core particle
    • Complex: BRCA1-UbcH5c/BARD1 E3-E2 module
      • Protein or peptide: BRCA1,Ubiquitin-conjugating enzyme E2 D3
      • Protein or peptide: BRCA1-associated RING domain protein 1
    • Complex: Nucleosome core particleNucleosome
      • Protein or peptide: Histone H2A type 2-A
      • Protein or peptide: Histone H2B type 1-K
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • DNA: Widom 601 153-bp
      • DNA: Widom 601 153-bp
  • Ligand: ZINC ION
KeywordsComplex / Ubiquitin / Nucleosome / RING / ligase / LIGASE-DNA complex
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / : / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication ...negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / : / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / (E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to indole-3-methanol / homologous recombination / lateral element / tissue homeostasis / XY body / protein K6-linked ubiquitination / Signaling by BMP / regulation of DNA damage checkpoint / regulation of phosphorylation / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / protein K11-linked ubiquitination / : / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / DNA-binding transcription activator activity / intracellular non-membrane-bounded organelle / ubiquitin conjugating enzyme activity / Transcriptional Regulation by E2F6 / protein monoubiquitination / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of BMP signaling pathway / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / protein K48-linked ubiquitination / localization / negative regulation of megakaryocyte differentiation / regulation of DNA repair / protein autoubiquitination / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / Packaging Of Telomere Ends / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / positive regulation of DNA repair / 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 / tubulin binding / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / IKK complex recruitment mediated by RIP1 / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / male germ cell nucleus / Defective pyroptosis / Negative regulators of DDX58/IFIH1 signaling / chromosome segregation
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / BRCA1 C Terminus (BRCT) domain / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ring finger / 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 / Ankyrin repeats (3 copies) / Histone H3 signature 1. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Histone H3 signature 2. / Ankyrin repeat / Histone H3 / Histone H3/CENP-A / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Truncated breast and ovarian cancer susceptibility protein 1 / Histone H2B type 1-K / Breast cancer type 1 susceptibility protein / Ubiquitin-conjugating enzyme E2 D3 / Histone H4 / Histone H2A type 2-A / Histone H3.2 / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWitus SR / Burrell AL / Hansen JM / Farrell DP / Dimaio F / Kollman JM / Klevit RE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM088055 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1.
Authors: Samuel R Witus / Anika L Burrell / Daniel P Farrell / Jianming Kang / Meiling Wang / Jesse M Hansen / Alex Pravat / Lisa M Tuttle / Mikaela D Stewart / Peter S Brzovic / Champak Chatterjee / ...Authors: Samuel R Witus / Anika L Burrell / Daniel P Farrell / Jianming Kang / Meiling Wang / Jesse M Hansen / Alex Pravat / Lisa M Tuttle / Mikaela D Stewart / Peter S Brzovic / Champak Chatterjee / Weixing Zhao / Frank DiMaio / Justin M Kollman / Rachel E Klevit /
Abstract: Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme ...Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system. The structure reveals that a novel BARD1-histone interface couples to a repositioning of UbcH5c compared to the structurally similar PRC1 E3 ligase Ring1b/Bmi1 that ubiquitylates H2A Lys119 in nucleosomes. This interface is sensitive to both H3 Lys79 methylation status and mutations found in individuals with cancer. Furthermore, NMR reveals an unexpected mode of E3-mediated substrate regulation through modulation of dynamics in the C-terminal tail of H2A. Our findings provide insight into how E3 ligases preferentially target nearby lysine residues in nucleosomes by a steric occlusion and distancing mechanism.
History
DepositionSep 2, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.8
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  • Surface view with fitted model
  • Atomic models: PDB-7jzv
  • Surface level: 0.8
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22581.png

Downloads & links

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Map

FileDownload / File: emd_22581.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBRCA1-UbcH5c/BARD1 E3-E2 module bound to the nucleosome core particle
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.8
Minimum - Maximum-11.7770815 - 14.925698000000001
Average (Standard dev.)-0.000000000000861 (±0.341186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-11.77714.926-0.000

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Supplemental data

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Mask #1

Fileemd_22581_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_22581_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_22581_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BRCA1-UbcH5c/BARD1 E3-E2 module bound to nucleosome core particle

EntireName: BRCA1-UbcH5c/BARD1 E3-E2 module bound to nucleosome core particle
Components
  • Complex: BRCA1-UbcH5c/BARD1 E3-E2 module bound to nucleosome core particle
    • Complex: BRCA1-UbcH5c/BARD1 E3-E2 module
      • Protein or peptide: BRCA1,Ubiquitin-conjugating enzyme E2 D3
      • Protein or peptide: BRCA1-associated RING domain protein 1
    • Complex: Nucleosome core particleNucleosome
      • Protein or peptide: Histone H2A type 2-A
      • Protein or peptide: Histone H2B type 1-K
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • DNA: Widom 601 153-bp
      • DNA: Widom 601 153-bp
  • Ligand: ZINC ION

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Supramolecule #1: BRCA1-UbcH5c/BARD1 E3-E2 module bound to nucleosome core particle

SupramoleculeName: BRCA1-UbcH5c/BARD1 E3-E2 module bound to nucleosome core particle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: BRCA1-UbcH5c/BARD1 E3-E2 module

SupramoleculeName: BRCA1-UbcH5c/BARD1 E3-E2 module / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BRCA1,Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: BRCA1,Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.974465 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPDLSALRVE EVQNVINAMQ KILECPICLE LIKEPVSTKC DHIFCKFCML KLLNQKKGPS QCPLCKNDIT KRSLQESTRF SQLVEELLK IICAFQLDTG LEYANSGSGS GSGALKRINK ELSDLARDPP AQCSAGPVGD DMFHWQATIM GPNDSPYQGG V FFLTIHFP ...String:
GPDLSALRVE EVQNVINAMQ KILECPICLE LIKEPVSTKC DHIFCKFCML KLLNQKKGPS QCPLCKNDIT KRSLQESTRF SQLVEELLK IICAFQLDTG LEYANSGSGS GSGALKRINK ELSDLARDPP AQCSAGPVGD DMFHWQATIM GPNDSPYQGG V FFLTIHFP TDYPFKPPKV AFTTRIYHPN INSNGSIKLD ILRSQWSPAL TISKVLLSIC SLLCDPNPDD PLVPEIARIY KT DRDKYNR ISREWTQKYA M

UniProtKB: Truncated breast and ovarian cancer susceptibility protein 1, Ubiquitin-conjugating enzyme E2 D3

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Macromolecule #2: BRCA1-associated RING domain protein 1

MacromoleculeName: BRCA1-associated RING domain protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.983018 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MEPDGRGAWA HSRAALDRLE KLLRCSRCTN ILREPVCLGG CEHIFCSNCV SDCIGTGCPV CYTPAWIQDL KINRQLDSMI QLCSKLRNL LHDNELSDLK EDKPRKSLFN DAGNKK

UniProtKB: BRCA1-associated RING domain protein 1

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Macromolecule #3: Histone H2A type 2-A

MacromoleculeName: Histone H2A type 2-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.310728 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GAMGSGRGKQ GGKARAKAKS RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYMAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGKVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 2-A

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.790018 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-K

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Macromolecule #5: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.257838 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #7: Widom 601 153-bp

MacromoleculeName: Widom 601 153-bp / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 47.457234 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DA)(DT)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT) (DG)(DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG) (DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC) (DG)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG)(DA) (DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG) (DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DA)(DT)

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Macromolecule #8: Widom 601 153-bp

MacromoleculeName: Widom 601 153-bp / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.998945 KDa
SequenceString: (DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA) ...String:
(DA)(DT)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG) (DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT)(DG)(DT) (DC)(DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC) (DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT) (DA)(DG)(DT)(DC)(DT) (DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DT)(DG)(DA)(DT)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHEPES-NaOH
35.0 mMNaClSodium chloride
1.0 mMDTT
GridModel: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 2 / Average exposure time: 10.0 sec. / Average electron dose: 90.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSparc ab initio 3D reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21479
FSC plot (resolution estimation)

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