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- PDB-8tw2: Acinetobacter phage AP205 T=4 VLP -

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Basic information

Entry
Database: PDB / ID: 8tw2
TitleAcinetobacter phage AP205 T=4 VLP
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / Acinetobacter / SsRNA phage virus / VIRUS / VLP
Function / homologyviral capsid / Coat protein
Function and homology information
Biological speciesAcinetobacter phage AP205 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 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 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Coat protein
AB: Coat protein
AC: Coat protein
AD: 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
AR: 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
BR: 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
CR: 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
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
DP: Coat protein
DQ: Coat protein
DR: 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
ER: 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
FR: 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
GK: Coat protein
GL: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GP: Coat protein
GQ: Coat protein
GR: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GV: Coat protein
GW: Coat protein
GX: Coat protein
GY: Coat protein
GZ: Coat protein
HA: Coat protein
HB: Coat protein
HC: Coat protein
HD: Coat protein
HE: Coat protein
HF: Coat protein
HG: Coat protein
HI: Coat protein
HJ: Coat protein
HK: Coat protein
HL: Coat protein
HM: Coat protein
HN: Coat protein
HO: Coat protein
HP: Coat protein
HQ: Coat protein
HR: Coat protein
HS: Coat protein
HT: Coat protein
HU: Coat protein
HV: Coat protein
HW: Coat protein
HX: Coat protein
HY: Coat protein
HZ: Coat protein
IA: Coat protein
IB: Coat protein
IC: Coat protein
ID: Coat protein
IE: Coat protein
IF: Coat protein
IG: Coat protein
IH: Coat protein
II: Coat protein
IJ: Coat protein
IK: Coat protein
IL: Coat protein
IM: Coat protein
IN: Coat protein
IO: Coat protein
IP: Coat protein
IQ: Coat protein
IR: Coat protein
IS: Coat protein
IT: Coat protein
IU: Coat protein
IV: Coat protein
IW: Coat protein
IX: Coat protein
IZ: Coat protein
JA: Coat protein
JB: Coat protein
JC: Coat protein
JD: Coat protein
JE: Coat protein
JF: Coat protein
JG: Coat protein
JH: Coat protein
JI: Coat protein
JJ: Coat protein


Theoretical massNumber of molelcules
Total (without water)3,316,937240
Polymers3,316,937240
Non-polymers00
Water0
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 ...
Coat protein


Mass: 13820.569 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Source: (natural) Acinetobacter phage AP205 (virus) / References: UniProt: Q9AZ42

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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: all / Source: NATURAL
Molecular weightValue: 3.3 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: 300 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-HClTris1
2150 mMsodium chlorideNaClSodium chloride1
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 FIELDBright-field microscopy / 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: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005236400
ELECTRON MICROSCOPYf_angle_d0.608322080
ELECTRON MICROSCOPYf_dihedral_angle_d4.69132640
ELECTRON MICROSCOPYf_chiral_restr0.04238400
ELECTRON MICROSCOPYf_plane_restr0.00441760

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