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- PDB-8tob: Acinetobacter GP16 Type IV pilus -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8tob
TitleAcinetobacter GP16 Type IV pilus
Components(Fimbrial protein) x 2
KeywordsCELL ADHESION / T4P / Competence
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane
Similarity search - Function
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
Biological speciesAcinetobacter genomosp. 16BJ (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsMeng, R. / Xing, Z. / 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 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
GA: Fimbrial protein
HA: Fimbrial protein
IA: Fimbrial protein
JA: Fimbrial protein
KA: Fimbrial protein
LA: Fimbrial protein
MA: Fimbrial protein
NA: Fimbrial protein
OA: Fimbrial protein
PA: Fimbrial protein
QA: Fimbrial protein
RA: Fimbrial protein
SA: Fimbrial protein
TA: Fimbrial protein
UA: Fimbrial protein
VA: Fimbrial protein
AA: Fimbrial protein
BA: Fimbrial protein
CA: Fimbrial protein
DA: Fimbrial protein
EA: Fimbrial protein
FA: Fimbrial protein
GB: Fimbrial protein
HB: Fimbrial protein
IB: Fimbrial protein
JB: Fimbrial protein
KB: Fimbrial protein
LB: Fimbrial protein
MB: Fimbrial protein
NB: Fimbrial protein
OB: Fimbrial protein
PB: Fimbrial protein
QB: Fimbrial protein
RB: Fimbrial protein
SB: Fimbrial protein
TB: Fimbrial protein
UB: Fimbrial protein
VB: Fimbrial protein
AB: Fimbrial protein
BB: Fimbrial protein
CB: Fimbrial protein
DB: Fimbrial protein
EB: Fimbrial protein
FB: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)318,35244
Polymers318,35244
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 ...
Fimbrial protein


Mass: 7470.747 Da / Num. of mol.: 22 / Fragment: residues 9-78 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9
#2: Protein ...
Fimbrial protein


Mass: 6999.778 Da / Num. of mol.: 22 / Fragment: residues 79-147 / Source method: isolated from a natural source / Source: (natural) Acinetobacter genomosp. 16BJ (bacteria) / References: UniProt: N9RQW9
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Acinetobacter genomosp.16 Tyoe IV pilus / Type: COMPLEX / Details: Filamentous Type IV pilus / Entity ID: all / Source: NATURAL
Molecular weightValue: 11 kDa/nm / Experimental value: NO
Source (natural)Organism: Acinetobacter genomosp. 16BJ (bacteria)
Buffer solutionpH: 8 / Details: 20mM Tris-HCl, 200mM NaCl, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris (hydroxymethyl) aminomethane (THAM) hydrochlorideTris-HCl1
2200 mMSodium ChlorideNaCl1
SpecimenConc.: 1.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: vitreous Typy IV pilus
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 QuantiFoil R2/1 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: 135000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 92 ° / Axial rise/subunit: 10 Å / Axial symmetry: C1
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 900000 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222528
ELECTRON MICROSCOPYf_angle_d0.42830712
ELECTRON MICROSCOPYf_dihedral_angle_d3.9923146
ELECTRON MICROSCOPYf_chiral_restr0.0383916
ELECTRON MICROSCOPYf_plane_restr0.0033784

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