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- PDB-8tva: Outer Mat-T4P complex -

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Basic information

Entry
Database: PDB / ID: 8tva
TitleOuter Mat-T4P complex
Components
  • (Fimbrial protein) x 2
  • Maturation protein
KeywordsVIRUS / Acinetobacter / SsRNA phage virus / T4P
Function / homology
Function and homology information


virion attachment to host cell pilus / protein secretion by the type II secretion system / type II protein secretion system complex / pilus / virion component / cell adhesion / membrane
Similarity search - Function
Assembly protein / Phage maturation protein / Bacterial general secretion pathway protein G-type pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Fimbrial protein / Maturation protein
Similarity search - Component
Biological speciesAcinetobacter phage AP205 (virus)
Acinetobacter genomosp. 16BJ (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.55 Å
AuthorsMeng, R. / Xing, Z. / Thongchol, 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 17, 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 1.2Oct 9, 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
b: Maturation protein
BK: Fimbrial protein
BL: Fimbrial protein
BM: Fimbrial protein
BN: Fimbrial protein
BO: Fimbrial protein
BP: Fimbrial protein
BQ: Fimbrial protein
BR: Fimbrial protein
BS: Fimbrial protein
BT: Fimbrial protein
BU: Fimbrial protein
BV: Fimbrial protein
BW: Fimbrial protein
BX: Fimbrial protein
BY: Fimbrial protein
BZ: Fimbrial protein
CA: Fimbrial protein
CB: Fimbrial protein
CC: Fimbrial protein
CD: Fimbrial protein
CE: Fimbrial protein
CF: Fimbrial protein
CG: Fimbrial protein
CH: Fimbrial protein
CI: Fimbrial protein
CJ: Fimbrial protein
CK: Fimbrial protein
CL: Fimbrial protein
CM: Fimbrial protein
CN: Fimbrial protein
CO: Fimbrial protein
CP: Fimbrial protein
CQ: Fimbrial protein
CR: Fimbrial protein
CS: Fimbrial protein
CT: Fimbrial protein
CU: Fimbrial protein
CV: Fimbrial protein
CW: Fimbrial protein
CX: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)350,47441
Polymers350,47441
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: Protein Maturation protein


Mass: 61063.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ43
#2: Protein
Fimbrial protein


Mass: 7470.747 Da / Num. of mol.: 20 / Fragment: residues 9-78 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9
#3: Protein
Fimbrial protein


Mass: 6999.778 Da / Num. of mol.: 20 / Fragment: residues 79-147 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9
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 / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.378 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 Capsid / 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
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
9PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 8.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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