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- PDB-8fne: phiPA3 PhuN Tetramer, p2 -

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Basic information

Entry
Database: PDB / ID: 8fne
TitlephiPA3 PhuN Tetramer, p2
ComponentsMaltose/maltodextrin-binding periplasmic protein, PhuN
KeywordsVIRAL PROTEIN / phiPA3 protein / shell protein / PhuN / phage nucleus
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / host cell cytoplasm / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Chimallin / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Pseudomonas phage PhiPA3 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsNieweglowska, E.S. / Brilot, A.F. / Mendez-Moran, M. / Kokontis, C. / Baek, M. / Li, J. / Cheng, Y. / Baker, D. / Bondy-Denomy, J. / Agard, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)R35GM118099 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2023
Title: The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice.
Authors: Eliza S Nieweglowska / Axel F Brilot / Melissa Méndez-Moran / Claire Kokontis / Minkyung Baek / Junrui Li / Yifan Cheng / David Baker / Joseph Bondy-Denomy / David A Agard /
Abstract: To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host ...To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Å by cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules.
History
DepositionDec 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein, PhuN
B: Maltose/maltodextrin-binding periplasmic protein, PhuN
C: Maltose/maltodextrin-binding periplasmic protein, PhuN
D: Maltose/maltodextrin-binding periplasmic protein, PhuN
E: Maltose/maltodextrin-binding periplasmic protein, PhuN
F: Maltose/maltodextrin-binding periplasmic protein, PhuN
G: Maltose/maltodextrin-binding periplasmic protein, PhuN
H: Maltose/maltodextrin-binding periplasmic protein, PhuN


Theoretical massNumber of molelcules
Total (without water)881,0098
Polymers881,0098
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Fluorescence light microscopy was done, and has been previously published, to monitor the assembly of this protein in vivo., electron microscopy, The protein self-assembles into ...Evidence: microscopy, Fluorescence light microscopy was done, and has been previously published, to monitor the assembly of this protein in vivo., electron microscopy, The protein self-assembles into a large-scale 2D crystalline array when applied to glow-discharged grids for negative stain EM at pH 6.5 but appears as monomers or individual, smaller assemblies at pH 7.5.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein, PhuN / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / ChmA / Phage nucleus ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / ChmA / Phage nucleus enclosure protein / PhuN / gene product 53 / gp53


Mass: 110126.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Pseudomonas phage PhiPA3 (virus)
Gene: malE, b4034, JW3994, 053 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P0AEX9, UniProt: F8SJT5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Core tetramer assembly (p2) of the phiPA3 bacteriophage PhuN protein
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas phage PhiPA3 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 Star (DE3)pLysS
Buffer solutionpH: 6.5
Details: 0.25 cOmplete Protease Inhibitor Tablet also included
Buffer component
IDConc.NameBuffer-ID
120 mMBisTrisPropane1
2150 mMSodium Chloride1
31 mMDTT1
41 mMEDTA1
52 mMMagnesium Chloride1
61 mMATP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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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: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
ISOLDE1.2.2model building
UCSF ChimeraX1.2/v9model building
EM software
IDNameVersionCategoryDetails
1cryoSPARCv2.15.0particle selection
2cryoSPARCv3.3.1particle selection
4SerialEMv.3.6-v.3.8image acquisition
9Rosettamodel fittingRosettaRelax
10UCSF ChimeraXmodel fitting
11UCSF Chimeramodel fitting
14Rosettamodel refinementRosettaRefine
15ISOLDE1.2.1model refinement
16cryoSPARCv2.15.0initial Euler assignmentAb-Initio Reconstruction
18cisTEM1.0.0-betafinal Euler assignment
20cisTEM1.0.0-betaclassification
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29303 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: The initial model was generated using AlphaFold based on sequence alone.
Atomic model buildingSource name: AlphaFold / Type: in silico model

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