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- PDB-7rw6: BORF2-APOBEC3Bctd Complex -

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Basic information

Entry
Database: PDB / ID: 7rw6
TitleBORF2-APOBEC3Bctd Complex
Components
  • DNA dC->dU-editing enzyme APOBEC-3B
  • Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
KeywordsOXIDOREDUCTASE/HYDROLASE / Host-pathogen complex / viral protein / antiviral protein / deaminase / OXIDOREDUCTASE-HYDROLASE complex
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / release from viral latency / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...mRNA Editing: C to U Conversion / Formation of the Editosome / release from viral latency / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / retrotransposon silencing / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA demethylation / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / P-body / outer membrane-bounded periplasmic space / defense response to virus / DNA replication / periplasmic space / innate immune response / DNA damage response / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Ribonucleotide reductase large subunit, Alphaherpesviruses / Novel AID APOBEC clade 2 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / APOBEC/CMP deaminase, zinc-binding ...Ribonucleotide reductase large subunit, Alphaherpesviruses / Novel AID APOBEC clade 2 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase large subunit / Maltose/maltodextrin-binding periplasmic protein / DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Human gammaherpesvirus 4 (Epstein-Barr virus)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsShaban, N.M. / Yan, R. / Shi, K. / McLellan, J.S. / Yu, Z. / Harris, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) 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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
B: DNA dC->dU-editing enzyme APOBEC-3B
C: Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit
D: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,6326
Polymers317,5014
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Ribonucleoside-diphosphate reductase large subunit / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / R1 / Ribonucleotide reductase ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / R1 / Ribonucleotide reductase large subunit


Mass: 133408.031 Da / Num. of mol.: 2 / Mutation: K-131A, N -197A, E -198A, K-287A, D-288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: K12 / Gene: malE, b4034, JW3994, RIR1, BORF2 / Production host: Homo sapiens (human)
References: UniProt: P0AEX9, UniProt: P03190, ribonucleoside-diphosphate reductase
#2: Protein DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 25342.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Homo sapiens (human)
References: UniProt: Q9UH17, single-stranded DNA cytosine deaminase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1BORFf2/APOBEC3BctdCOMPLEX#1-#20MULTIPLE SOURCES
2MBP-BORF2 (large subunit of EBV ribonucleotide reductase with n-terminal MBP tag)COMPLEX#11RECOMBINANT
3APOBEC3Bctd-mychis (human APOBEC3B protein with c-terminal mychis tag)COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Homo sapiens (human)9606
32Epstein-Barr virus (Epstein-Barr virus)10376
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Homo sapiens (human)9606
22Homo sapiens (human)9606
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4486: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243192 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313458
ELECTRON MICROSCOPYf_angle_d0.54918234
ELECTRON MICROSCOPYf_dihedral_angle_d11.5884848
ELECTRON MICROSCOPYf_chiral_restr0.0411950
ELECTRON MICROSCOPYf_plane_restr0.0042360

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