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- PDB-9u04: LX-2D6 (Fab) - Polio 1 (VLP) complex -

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Basic information

Entry
Database: PDB / ID: 9u04
TitleLX-2D6 (Fab) - Polio 1 (VLP) complex
Components
  • (Capsid protein ...) x 3
  • LX-2D6 Fab Heavy chain
  • LX-2D6 Fab Light chain
KeywordsVIRUS LIKE PARTICLE / Capsid protein / virus-like particle / complex / vaccine / monoclonal antibody / Fab
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / host cell cytoplasm / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / virion attachment to host cell / host cell nucleus / structural molecule activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1 Mahoney
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.7 Å
AuthorsBahar, M.W. / Fry, E.E. / Stuart, D.I.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationRG.IMCB.I8-TSA-083 United States
CitationJournal: To Be Published
Title: LX-2D6 (Fab) - Polio 1 (VLP) complex
Authors: Bahar, M.W. / Stonehouse, N.J. / Rowlands, D.J. / Fry, E.E. / Stuart, D.I.
History
DepositionJan 26, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
H: LX-2D6 Fab Heavy chain
L: LX-2D6 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,6667
Polymers173,1815
Non-polymers4852
Water7,819434
1
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
H: LX-2D6 Fab Heavy chain
L: LX-2D6 Fab Light chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)10,419,946420
Polymers10,390,858300
Non-polymers29,088120
Water5,405300
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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Capsid protein ... , 3 types, 3 molecules ABC

#1: Protein Capsid protein VP1 / P1D / Virion protein 1


Mass: 33447.586 Da / Num. of mol.: 1 / Mutation: VP1 H248P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Production host: Komagataella pastoris (fungus) / References: UniProt: P03300
#2: Protein Capsid protein VP0 / VP4-VP2


Mass: 37334.613 Da / Num. of mol.: 1 / Mutation: VP2 T25A, VP2 D57E, VP4 R18G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Production host: Komagataella pastoris (fungus) / References: UniProt: P03300
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26550.549 Da / Num. of mol.: 1 / Mutation: VP3 L119M, VP3 Q178L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Production host: Komagataella pastoris (fungus) / References: UniProt: P03300

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Antibody , 2 types, 2 molecules HL

#4: Antibody LX-2D6 Fab Heavy chain


Mass: 50983.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full sequence for the heavy chain of monoclonal antibody LX-2D6
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hybridoma cell line / Production host: Homo sapiens (human)
#5: Antibody LX-2D6 Fab Light chain


Mass: 24864.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full sequence for the light chain of monoclonal antibody LX-2D6
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Hybridoma cell line / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 436 molecules

#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: Human poliovirus 1 Mahoney / Type: VIRUS
Details: Recombinantly expressed virus-like particle of poliovirus type 1 Mahoney strain.
Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 5.84 MDa / Experimental value: NO
Source (natural)Organism: Human poliovirus 1 Mahoney / Strain: Mahoney
Source (recombinant)Organism: Komagataella pastoris (fungus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Virus shell 1 / Diameter: 310 nm / Triangulation number (T number): 1
Buffer solutionpH: 7 / Details: 1 x DPBS, 20 mM EDTA, pH 7.0
Buffer component
IDConc.NameBuffer-ID
11 xDPBS1
220 mMEDTA1
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample purified by sucrose density gradient ultracentrifugation. Concentrated sample mixed with Fab to form complex.
Specimen supportDetails: Exact grid type was Quantifoil R2/1 Cu grids with 2 nm continous carbon layer. Product no. AGS174-1-2CL, Agar Scientific.
Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278.15 K
Details: 3 ul of sample blotted for 3.5 seconds with -10 blot force on FEI Vitrobot mark IV.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Calibrated pixel size was 0.7303 A/pix.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.79 sec. / Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12000
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.3.1particle selectionTemplate picker
2PHENIX1.21.2_5419model refinement
5cryoSPARC4.3.1CTF correctionPatch CTF
10cryoSPARC4.3.1initial Euler assignmentAb-initio reconstruction
11cryoSPARC4.3.1final Euler assignmentHomogeneous refinement
12cryoSPARC4.3.1classificationHeterogeneous refinement
13cryoSPARC4.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 190028
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 1.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105643 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using phenix_real.space.refine.
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails (eV)
11HXS

1hxs

1HXS1PDBexperimental model
2AlphaFoldin silico modelAlphaFold model for Fab
RefinementHighest resolution: 1.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00450340
ELECTRON MICROSCOPYf_angle_d0.5568580
ELECTRON MICROSCOPYf_dihedral_angle_d10.88618234
ELECTRON MICROSCOPYf_chiral_restr0.0457638
ELECTRON MICROSCOPYf_plane_restr0.0048838

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