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- EMDB-24715: Focused Refined Map BORF2-APOBEC3Bctd Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24715
TitleFocused Refined Map BORF2-APOBEC3Bctd Complex
Map dataFocused Refined Sharpened Map
Sample
  • Complex: BORF2/APOBEC3Bctd
    • Complex: MBP-BORF2
    • Complex: APOBEC3Bctd-mychis
Biological speciesEpstein-Barr virus (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsShaban NM / Yan R / Shi K / McLellan JS / Yu Z / Harris RS
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA234228 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56-AI150402 United States
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition.
Authors: Nadine M Shaban / Rui Yan / Ke Shi / Sofia N Moraes / Adam Z Cheng / Michael A Carpenter / Jason S McLellan / Zhiheng Yu / Reuben S Harris /
Abstract: Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide ...Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000-Å binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.
History
DepositionAug 19, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateMay 11, 2022-
Current statusMay 11, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24715.png

Downloads & links

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Map

FileDownload / File: emd_24715.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused Refined Sharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 336 pix.
= 283.584 Å		0.84 Å/pix.
x 336 pix.
= 283.584 Å		0.84 Å/pix.
x 336 pix.
= 283.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.0021839016 - 2.0344691
Average (Standard dev.)0.0012007297 (±0.027719734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 283.58398 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened Map

Fileemd_24715_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_24715_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_24715_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BORF2/APOBEC3Bctd

EntireName: BORF2/APOBEC3Bctd
Components
  • Complex: BORF2/APOBEC3Bctd
    • Complex: MBP-BORF2
    • Complex: APOBEC3Bctd-mychis

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Supramolecule #1: BORF2/APOBEC3Bctd

SupramoleculeName: BORF2/APOBEC3Bctd / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: MBP-BORF2

SupramoleculeName: MBP-BORF2 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Epstein-Barr virus (Epstein-Barr virus)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: APOBEC3Bctd-mychis

SupramoleculeName: APOBEC3Bctd-mychis / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243192
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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