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- EMDB-41443: Acinetobacter phage AP205 -

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Basic information

Entry
Database: EMDB / ID: EMD-41443
TitleAcinetobacter phage AP205
Map datamain map
Sample
  • Virus: Acinetobacter phage AP205 (virus)
    • RNA: RNA (4269-MER)
    • Protein or peptide: Coat protein
    • Protein or peptide: Maturation protein
KeywordsAcinetobacter / SsRNA phage virus / VIRUS / VIRUS-RNA complex
Function / homologyAssembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / viral capsid / Coat protein / Maturation protein
Function and homology information
Biological speciesBacteria abnormis (insect) / Acinetobacter phage AP205 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsMeng R / Xing Z / Chang J / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01GM141659 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis of Acinetobacter type IV pili targeting by an RNA virus.
Authors: Ran Meng / Zhongliang Xing / Jeng-Yih Chang / Zihao Yu / Jirapat Thongchol / Wen Xiao / Yuhang Wang / Karthik Chamakura / Zhiqi Zeng / Fengbin Wang / Ry Young / Lanying Zeng / Junjie Zhang /
Abstract: Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. ...Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into the interaction between Acinetobacter phage AP205 and type IV pili. Using cryo-electron microscopy, we solve structures of the AP205 virion with an asymmetric dimer of maturation proteins, the native Acinetobacter type IV pili bearing a distinct post-translational pilin cleavage, and the pili-bound AP205 showing its maturation proteins adapted to pilin modifications, allowing each phage to bind to one or two pili. Leveraging these results, we develop a 20-kilodalton AP205-derived protein scaffold targeting type IV pili in situ, with potential for research and diagnostics.
History
DepositionAug 3, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41443.png

Downloads & links

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Map

FileDownload / File: emd_41443.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.30823332 - 1.7096045
Average (Standard dev.)0.02108636 (±0.121311165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 487.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map a

Fileemd_41443_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_41443_half_map_2.map
Annotationhalf map b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Acinetobacter phage AP205

EntireName: Acinetobacter phage AP205 (virus)
Components
  • Virus: Acinetobacter phage AP205 (virus)
    • RNA: RNA (4269-MER)
    • Protein or peptide: Coat protein
    • Protein or peptide: Maturation protein

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Supramolecule #1: Acinetobacter phage AP205

SupramoleculeName: Acinetobacter phage AP205 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Details: amplified and purified from infected Acinetobacter GP16 cells.
NCBI-ID: 154784 / Sci species name: Acinetobacter phage AP205 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Molecular weightTheoretical: 3.94 MDa
Virus shellShell ID: 1 / Name: Coat / Diameter: 290.0 Å / T number (triangulation number): 3

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Macromolecule #1: RNA (4269-MER)

MacromoleculeName: RNA (4269-MER) / type: rna / ID: 1 / Details: genomic RNA / Number of copies: 1
Source (natural)Organism: Bacteria abnormis (insect)
Molecular weightTheoretical: 1.368509375 MDa
SequenceString: GGAGUGAACC CCGGAGGGGG UUCGCUGAAA GCCGAAUCGA AUUCGACUUU GCGUGAUUCA CAUCACGUCU UACUCACGAU ACUAGUACC GCGAGUUAUC UUGUGGUAAU UAAAAACUAC CAGGAGAUAA CUUUAUGAAG AAAAGGACAA AAGCCUUGCU U CCCUAUGC ...String:
GGAGUGAACC CCGGAGGGGG UUCGCUGAAA GCCGAAUCGA AUUCGACUUU GCGUGAUUCA CAUCACGUCU UACUCACGAU ACUAGUACC GCGAGUUAUC UUGUGGUAAU UAAAAACUAC CAGGAGAUAA CUUUAUGAAG AAAAGGACAA AAGCCUUGCU U CCCUAUGC GGUUUUCAUC AUACUCAGCU UUCAACUAAC AUUGUUGACU GCCUUGUUUA UGUAUUACCA UUAUACCUUU UA GGAGAUG GUGUCAUGAA CAUGUACAAA UGGGUACCUG AAAGUAUCCG CGAUUCUGGC GAGGGGCAAC CCUCUUAUUC AAA UAAUGG UGAUUAUGCA CCGAGCGGCC CUUGGGUUGC UGCGGGUAUU CAUACCAUGC CACAAUCGCU GCGGGAUUCC AUGA GAAAU UCUAUCAUGG UCACCGCGCA AGCUCGUCGU GAUGUCAUUG GCCCCGAAUG GGGCCCUGAC GGACGCUUUA CUGGA UAUG CUUCAGUGAU CGGGACACCU GAUCCUAAGC CUGCUGAUAU UGUGAACAAG UUUACAGUUG AACGCAGACC GGUCAG CAA CGGAAAUUUU CAACAGCGUG UGAAAGCUGG UGACAUUGUU GUUGCACCGU AUACCAGUGA UGGAAAGAUU ACUGUUA AA CUAGUCGCCG GUCAGAAGGA CAUUUCAAGU ACUCCUGAUU ACGAUUAUCG AAUUGACAGU AGUUUGGCGU CAUCCGCC G GAUUUGUUGU UGCUGGUGAA CGUUGGUAUU AUACCAAACG UCACUUCAUU AUCCCUCGUU ACUUCCAAAA CUGGCGCAU GCGCCGGCGU AAGUACGUAA CUGGUUGGGU AAUGCCAACG UUUUAUAGUC CGAAAGAGAU UUUUAAUCGC CUUAAGGAUU CGUUGGUAC CAGAUACUGG GUUAGUCACC CAAGUUUGGG CAGACAACAA CACAAAACGG AUGGAUUUCC UCACCGCUAU G GCUGAAAU CCCACAGACU CUCUCUUCUU UUCUCGAUGC GUUGGGUUAC CUCGGAUCGC UUAUUAAAGA UUUUAAACGU CG UCGCUUC UUUUUAAAUA AAGCGCAUCA ACGUAUCCGU AAUAAGCUCG GGGUGUCUUU CGCAGAAAGA AGAUCACAAA UUG UAUCUA AGUACGAUCG UAAGAUCGCA UCUGCCCGUA AGCCUGCAAU UAUUGUAAAA UUGCGGCAAC GGAAAGAAAA GGCC UUAAA AGCCCUAGAU AAAAUGCGUG UUCGAGAGGA AAAGAAAAUG AUACGUGAAU UUGCCACUCA GGCAGCCUCA CUAUG GCUU UCUUUUCGGU ACGAGAUCAU GCCGCUUUAU UAUCAAUCUC AGGACGUAUU GGACGUAAUU GCCAACUCGA CUUCUG AAU UUAUGACAUC GCGGGACUUU GUUGCUAAAG CAAUCAACAU UGGAAUUCCU UUGGAAUGGA AUCUUGAUCA AGAAAAC UU GGUUUCUCAA CCGAGACACA AUGUGAUGGU UAAAUCAAAA UUGUCACCCG AAAACAACAU CGGGAAGACU CUUUCAGU U AAUCCAUUUA CAACAGCUUG GGAGCUGUUG ACAUUGUCCU UCGUCGUCGA CUGGUUUGUC AACUUUGGUG ACGUCAUCG CAGGGUUUAC UGGCGGUUAC UCAGAUGAUU CUGGGGCAAC UGCUAGUUGG CGCUUUGAUG AUAAAAAGGU AUUCCACUUA AAGAAUAUC CCCUCAGCUA UGGUGAUCGU CGACAUUAAC UUCUACACCC GUCAGGUCAU UGACCCGCGG CUGUGCGGGG G GCUUGCUU UCUCCCCCAA ACUUAACCUU UUCCGGUAUC UUGACGCCAU GAGUUUAUCA UGGAAUCGAU CUCGUUUAAA GA UCAGUCG AGCUACUUGA CAAUUUUCUG CGCACCCAUC CCGGGUGGCG CCCAAAGUGA GGAAAAUCAC AUGGCAAAUA AGC CAAUGC AACCGAUCAC AUCUACAGCA AAUAAAAUUG UGUGGAGUGA UCCAACUCGU UUAUCAACUA CAUUUUCAGC AAGU CUGUU ACGCCAACGU GUUAAAGUUG GUAUAGCCGA ACUGAAUAAU GUUUCAGGUC AAUAUGUAUC UGUUUAUAAG CGUCC UGCA CCUAAACCGG AAGGUUGUGC AGAUGCCUGU GUCAUUAUGC CGAAUGAAAA CCAAUCCAUU CGCACAGUGA UUUCAG GGU CAGCCGAAAA CUUGGCUACC UUAAAAGCAG AAUGGGAAAC UCACAAACGU AACGUUGACA CACUCUUCGC GAGCGGC AA CGCCGGUUUG GGUUUCCUUG ACCCUACUGC GGCUAUCGUA UCGUCUGAUA CUACUGCUUA AGUGGUGAUU ACUGUGCC U AAAAGUCAAA AUAAACGACA AAUAAGACGC AGUUCUUCCG UUAAUUACAA GAAUAUCGUU AAAGCUUGCA AUGAUGCAA UGCUAAACGC UUGUGAUCAA CUGAAGUCCA CGAGUAUUCC UGCUUUCCAA UCAAACGUCC UUUCGGAUGU UCUUUCCCUC UCUGAUGCG GCCGACAUAA CAGUCAAGCA CCGAAUUGUU UCUAAAUUCG GCGAGCCUGC UGGGUCGAGC CUCCGCGACG U UGCUUUUA ACAAUUAUAA AUUGUUCGAA CAACAUCUUG GGAGCAUUCC UCAGAUUACU AAUCUGUGGC AGGAAGGAAA AG AGUUUUU CUUUUUGCGG AAAGCAAAGG CUAACUUGGG UAAAUGGUUA AAAACAUUUA AACUUGACUA UAAUUCUAUU ACA GUCGAG UUCACCCCAG GUGAGUCUUA UACCUCGGCC ACUGGGCACG UAUCGGUGUU UGCUAAGCUU UCCAACUUAG CUCA CUGGA CAUGCACUGC UGACGUCGUU GAUGAUGUUU GCCAUCUAGU GUAUUAUAAU CGCGGCCUAA AGGCUGCCGC UAGAA AACA CAUCGGUCUG AUGGUCCCAA UUGAGGGAGA GUCUGGGUUU GACACCUUUU CUCGCCACCU CAUGGGUGUU AUAUCC AUC GUUCCUGGGG CCCGCGGCGC AUCCGUGCCG AAGAACCAGG AAACGGACCG UUUUAUCGAC GUUGAACCCA CUUUCAA UA UGAUUCUCCA GCGUUGGGUA GCGGGCGAAA UUACUCGCUG CUUAACUUUA GCUAAGAAUC AUCUUGGCGC AUCACGGA A UAUUAACGGU AAAGUUGUAU UUCACGAUGC UCAAGAAUUG CACAAAGAAA UGAUCCGAGA UCUUUCUUAU GCUACUAUU GAUUUUUCAA ACGCUUCUGA UAGCGUCUUG CUGUGGGUGG UACAGCUUCU UUUUCCGAAG CAUGUAUCGU AUGUUUUGAC ACAGUAUCG UUCGUCGACU GUCCAACUCG GUUCAGAUCU UAUCGAACCG AAUAAACUUU CAAGUAUGGG AAAUGGUUUU A CUUUUGAA GUAAUGACCC UCCUCUUACU GUCGAUAGGU AGAAUCUUUG AUCCUACCUG CCGGGUUUAC GGAGAUGAUG UU AUCAUCA AAGCAGAAGU AGCCGACGAU UUCAUCAACA CUGUGUCAUC CAUUGCCUUC AUGACGAACA AUAAGAAGAC CUU UUUGAA GGGUCUCUUU CGUGAAUCAU GCGGUGCUUU CCAAUUUGAC ACAUUUGACA UCCAGUCAUU UGAGUUCGAA UGGG CUGAU AAUUUUACUG ACGUUAUUGC GAUCUGCAAC AAACUGAAGU UAAUUAUCGA CGCUGCUCAA UGCAACGAAG CAGUA AUAG CAAUAUUACG CAAUGCGCAU ACCGUCAUCU GUGAAUGCAU CCCUGUUCUU UGCAAGGGAC CGCAGCCGCC UGAUUU CAA CCUCUUUUUA UCUCAAUAUG UUUAUGAUGA UAAUUGGAAG AAGAAACAGA UGAAAUCUGA UUUAGCCAUA ACUAAGC UA AAUAGACUCG UUGAUAAACA AUGGGGUUUC UUUUCAGCUA CACAUCAUCA CCCUGAGGAA UUAUGUUACG UAAACAUU C CUGUUUACGU CCCUCGUCGU GAUUCUGUUC AUGCUGGCCA GAAUCUUUUC GUUGACCUUU CAAAUCUUUA CGCUUUACG UUUUACCAAA UCAACGGUAA GAGGUAAAGG UAAAUGGGUC AAUGUUCCCC ACUGGGUUAC ACCGGUUGGU UCAAUUUAUC GUGCUUCCC GUAUCAGACA GCAAUACCCU AACAUAGGGG AAUUGCCUAC CUGCUACUGG UCACCACAUC AGUUGGACUU G AUCACCUC CUAAUAAAUC UUUACGAUUU AUAAUAAUGG UAUGUACUAU GAGUAUGUAU GUAGGUUGAA AACCCUACCC GC UUAGGAU UGCUUAGCAG UCCUUCCCGG CA

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Macromolecule #2: Maturation protein

MacromoleculeName: Maturation protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Molecular weightTheoretical: 61.063852 KDa
SequenceString: MNMYKWVPES IRDSGEGQPS YSNNGDYAPS GPWVAAGIHT MPQSLRDSMR NSIMVTAQAR RDVIGPEWGP DGRFTGYASV IGTPDPKPA DIVNKFTVER RPVSNGNFQQ RVKAGDIVVA PYTSDGKITV KLVAGQKDIS STPDYDYRID SSLASSAGFV V AGERWYYT ...String:
MNMYKWVPES IRDSGEGQPS YSNNGDYAPS GPWVAAGIHT MPQSLRDSMR NSIMVTAQAR RDVIGPEWGP DGRFTGYASV IGTPDPKPA DIVNKFTVER RPVSNGNFQQ RVKAGDIVVA PYTSDGKITV KLVAGQKDIS STPDYDYRID SSLASSAGFV V AGERWYYT KRHFIIPRYF QNWRMRRRKY VTGWVMPTFY SPKEIFNRLK DSLVPDTGLV TQVWADNNTK RMDFLTAMAE IP QTLSSFL DALGYLGSLI KDFKRRRFFL NKAHQRIRNK LGVSFAERRS QIVSKYDRKI ASARKPAIIV KLRQRKEKAL KAL DKMRVR EEKKMIREFA TQAASLWLSF RYEIMPLYYQ SQDVLDVIAN STSEFMTSRD FVAKAINIGI PLEWNLDQEN LVSQ PRHNV MVKSKLSPEN NIGKTLSVNP FTTAWELLTL SFVVDWFVNF GDVIAGFTGG YSDDSGATAS WRFDDKKVFH LKNIP SAMV IVDINFYTRQ VIDPRLCGGL AFSPKLNLFR YLDAMSLSWN RSRLKISRAT

UniProtKB: Maturation protein

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Macromolecule #3: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 3 / Number of copies: 178 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Molecular weightTheoretical: 13.820569 KDa
SequenceString:
ANKPMQPITS TANKIVWSDP TRLSTTFSAS LLRQRVKVGI AELNNVSGQY VSVYKRPAPK PEGCADACVI MPNENQSIRT VISGSAENL ATLKAEWETH KRNVDTLFAS GNAGLGFLDP TAAIVSSDTT

UniProtKB: Coat protein

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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
Component:
ConcentrationFormulaName
20.0 mMTris-HClTrisTris (hydroxymethyl) aminomethane (THAM) hydrochloride
150.0 mMNaClSodium chloridesodium chloride

Details: 20mM Tris-HCl, 150mM NaCl, pH 8.0
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: 3uL sample applied to a 300-mesh 2/1 copper grid.
DetailsAP205 virion particle

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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: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 150000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8toc:
Acinetobacter phage AP205

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