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- PDB-8toc: Acinetobacter phage AP205 -

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Basic information

Entry
Database: PDB / ID: 8toc
TitleAcinetobacter phage AP205
Components
  • Coat protein
  • Maturation protein
  • RNA (4269-MER)
KeywordsVIRUS/RNA / Acinetobacter / SsRNA phage virus / VIRUS / VIRUS-RNA complex
Function / homology
Function and homology information


virion attachment to host cell pilus / virion component / viral capsid
Similarity search - Function
: / AP205 coat protein / Assembly protein / Phage maturation protein
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Coat protein / Maturation protein
Similarity search - Component
Biological speciesBacteria abnormis (insect)
Acinetobacter phage AP205 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsMeng, R. / Xing, Z. / Chang, J. / Zhang, J.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: 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
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA (4269-MER)
a: Maturation protein
b: Maturation protein
AB: Coat protein
AC: Coat protein
AE: Coat protein
AF: Coat protein
AG: Coat protein
AH: Coat protein
AI: Coat protein
AJ: Coat protein
AK: Coat protein
AL: Coat protein
AM: Coat protein
AN: Coat protein
AO: Coat protein
AP: Coat protein
AQ: Coat protein
Ac: Coat protein
AS: Coat protein
AT: Coat protein
AU: Coat protein
AV: Coat protein
AW: Coat protein
AX: Coat protein
AY: Coat protein
AZ: Coat protein
BA: Coat protein
BB: Coat protein
BC: Coat protein
BD: Coat protein
BE: Coat protein
BF: Coat protein
BG: Coat protein
BH: Coat protein
BI: Coat protein
BJ: Coat protein
BK: Coat protein
BL: Coat protein
BM: Coat protein
BN: Coat protein
BO: Coat protein
BP: Coat protein
BQ: Coat protein
Bc: Coat protein
BS: Coat protein
BT: Coat protein
BU: Coat protein
BV: Coat protein
BW: Coat protein
BX: Coat protein
BY: Coat protein
BZ: Coat protein
CA: Coat protein
CB: Coat protein
CC: Coat protein
CD: Coat protein
CE: Coat protein
CF: Coat protein
CG: Coat protein
CH: Coat protein
CI: Coat protein
CJ: Coat protein
CK: Coat protein
CL: Coat protein
CM: Coat protein
CN: Coat protein
CO: Coat protein
CP: Coat protein
CQ: Coat protein
Cc: Coat protein
CS: Coat protein
CT: Coat protein
CU: Coat protein
CV: Coat protein
CW: Coat protein
CX: Coat protein
CY: Coat protein
CZ: Coat protein
DA: Coat protein
DB: Coat protein
DC: Coat protein
DD: Coat protein
DE: Coat protein
DF: Coat protein
DG: Coat protein
DH: Coat protein
DI: Coat protein
DJ: Coat protein
DK: Coat protein
DL: Coat protein
DM: Coat protein
DN: Coat protein
DO: Coat protein
DQ: Coat protein
Dc: Coat protein
DS: Coat protein
DT: Coat protein
DU: Coat protein
DV: Coat protein
DW: Coat protein
DX: Coat protein
DY: Coat protein
DZ: Coat protein
EA: Coat protein
EB: Coat protein
EC: Coat protein
ED: Coat protein
EE: Coat protein
EF: Coat protein
EG: Coat protein
EH: Coat protein
EI: Coat protein
EJ: Coat protein
EK: Coat protein
EL: Coat protein
EM: Coat protein
EN: Coat protein
EO: Coat protein
EP: Coat protein
EQ: Coat protein
Ec: Coat protein
ES: Coat protein
ET: Coat protein
EU: Coat protein
EV: Coat protein
EW: Coat protein
EX: Coat protein
EY: Coat protein
EZ: Coat protein
FA: Coat protein
FB: Coat protein
FC: Coat protein
FD: Coat protein
FE: Coat protein
FF: Coat protein
FG: Coat protein
FH: Coat protein
FI: Coat protein
FJ: Coat protein
FK: Coat protein
FL: Coat protein
FM: Coat protein
FN: Coat protein
FO: Coat protein
FP: Coat protein
FQ: Coat protein
Fc: Coat protein
FS: Coat protein
FT: Coat protein
FU: Coat protein
FV: Coat protein
FW: Coat protein
FX: Coat protein
FY: Coat protein
FZ: Coat protein
GA: Coat protein
GB: Coat protein
GC: Coat protein
GD: Coat protein
GE: Coat protein
GF: Coat protein
GG: Coat protein
GH: Coat protein
GI: Coat protein
GJ: Coat protein
GK: Coat protein
GL: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GP: Coat protein
GQ: Coat protein
Gc: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GV: Coat protein
GW: Coat protein
GX: Coat protein
GY: Coat protein


Theoretical massNumber of molelcules
Total (without water)3,950,698181
Polymers3,950,698181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (4269-MER)


Mass: 1368509.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: genomic RNA / Source: (natural) Bacteria abnormis (insect)
#2: Protein Maturation protein


Mass: 61063.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ43
#3: Protein ...
Coat protein


Mass: 13820.569 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ42
Has protein modificationY

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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

ComponentName: Acinetobacter phage AP205 / Type: VIRUS
Details: amplified and purified from infected Acinetobacter GP16 cells.
Entity ID: #1, #3, #2 / Source: NATURAL
Molecular weightValue: 3.94 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Acinetobacter genomosp. 16BJ
Virus shellName: Coat / Diameter: 290 nm / Triangulation number (T number): 3
Buffer solutionpH: 8 / Details: 20mM Tris-HCl, 150mM NaCl, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris (hydroxymethyl) aminomethane (THAM) hydrochlorideTris-HCl1
2150 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: AP205 virion particle
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3uL sample applied to a 300-mesh 2/1 copper grid

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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 FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002285194
ELECTRON MICROSCOPYf_angle_d0.448408137
ELECTRON MICROSCOPYf_dihedral_angle_d11.15776624
ELECTRON MICROSCOPYf_chiral_restr0.03351105
ELECTRON MICROSCOPYf_plane_restr0.00436773

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