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- EMDB-56481: LX-2D6 (Fab) - Polio 1 (VLP) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-56481
TitleLX-2D6 (Fab) - Polio 1 (VLP) complex
Map dataUnsharpened map.
Sample
  • Virus: Human poliovirus 1 Mahoney
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: LX-2D6 Fab Heavy chain
    • Protein or peptide: LX-2D6 Fab Light chain
  • Ligand: PALMITIC ACID
  • Ligand: MYRISTIC ACID
  • Ligand: water
KeywordsCapsid protein / virus-like particle / complex / vaccine / monoclonal antibody / Fab / VIRUS LIKE PARTICLE
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
Biological speciesHuman poliovirus 1 Mahoney / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.7 Å
AuthorsBahar MW / Fry EE / Stuart DI
Funding support United States, 1 items
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 MW / Stonehouse NJ / Rowlands DJ / Fry EE / Stuart DI
History
DepositionJan 26, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56481.png

Downloads & links

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Map

FileDownload / File: emd_56481.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 896 pix.
= 654.349 Å		0.73 Å/pix.
x 896 pix.
= 654.349 Å		0.73 Å/pix.
x 896 pix.
= 654.349 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.27437907 - 0.93765825
Average (Standard dev.)0.0016395187 (±0.0373968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions896896896
Spacing896896896
CellA=B=C: 654.3488 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map.

Fileemd_56481_additional_1.map
AnnotationSharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map.

Fileemd_56481_half_map_1.map
AnnotationHalf map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map.

Fileemd_56481_half_map_2.map
AnnotationHalf map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human poliovirus 1 Mahoney

EntireName: Human poliovirus 1 Mahoney
Components
  • Virus: Human poliovirus 1 Mahoney
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: LX-2D6 Fab Heavy chain
    • Protein or peptide: LX-2D6 Fab Light chain
  • Ligand: PALMITIC ACID
  • Ligand: MYRISTIC ACID
  • Ligand: water

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Recombinantly expressed virus-like particle of poliovirus type 1 Mahoney strain.
NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.84 MDa
Virus shellShell ID: 1 / Name: Virus shell 1 / Diameter: 310.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 33.447586 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNPASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE ...String:
GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNPASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE KWDDYTWQTS SNPSIFYTYG TAPARISVPY VGISNAYSHF YDGFSKVPLK DQSAALGDSL YGAASLNDFG IL AVRVVND PNPTKVTSKI RVYLKPKHIR VWCPRPPRAV AYYGPGVDYK DGTLTPLSTK DLTTY

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 37.334613 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GAQVSSQKVG AHENSNGAYG GSTINYTTIN YYRDSASNAA SKQDFSQDPS KFTEPIKDVL IKTAPMLNSP NIEACGYSDR VLQLTLGNS TITAQEAANS VVAYGRWPEY LRDSEANPVD QPTEPEVAAC RFYTLDTVSW TKESRGWWWK LPDALRDMGL F GQNMYYHY ...String:
GAQVSSQKVG AHENSNGAYG GSTINYTTIN YYRDSASNAA SKQDFSQDPS KFTEPIKDVL IKTAPMLNSP NIEACGYSDR VLQLTLGNS TITAQEAANS VVAYGRWPEY LRDSEANPVD QPTEPEVAAC RFYTLDTVSW TKESRGWWWK LPDALRDMGL F GQNMYYHY LGRSGYTVHV QCNASKFHQG ALGVFAVPEM CLAGDSNTTT MHTSYQNANP GEKGGTFTGT FTPDNNQTSP AR RFCPVDY LLGNGTLLGN AFVFPHQIIN LRTNNCATLV LPYVNSLSID SMVKHNNWGI AILPLAPLNF ASESSPEIPI TLT IAPMCC EFNGLRNITL PRLQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 26.550549 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFM FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFM FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRL TIDDSFTEGG YISVFYQTRI VVPLSTPREM DILGFVSACN DFSVRLLRDT THIEQKALAQ

UniProtKB: Genome polyprotein

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Macromolecule #4: LX-2D6 Fab Heavy chain

MacromoleculeName: LX-2D6 Fab Heavy chain / type: protein_or_peptide / ID: 4
Details: Full sequence for the heavy chain of monoclonal antibody LX-2D6
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.983504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFGLSWLFL VAILKGVQCE VQLLESGGGM VQPGGSLRLS CAVSGFPLRS DAMSWVRQAP GKGLAWVSSI SDSGGSTYYA DSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCAKDY GGWSGFDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK ...String:
MAFGLSWLFL VAILKGVQCE VQLLESGGGM VQPGGSLRLS CAVSGFPLRS DAMSWVRQAP GKGLAWVSSI SDSGGSTYYA DSVKGRFTI SRDNSKNTLY LQMNSLRAED TAVYYCAKDY GGWSGFDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KS CDKTHTC PPCPAPELLG GPSVFLFPPK PKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKTKPREEQY NST YRVVSV LTVLHQDWLN GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVYTLPPSR EEMTKNQVSL TCLVKGFYPS DIAV EWESN GQPENNYKTT PPVLDSDGSF FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

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Macromolecule #5: LX-2D6 Fab Light chain

MacromoleculeName: LX-2D6 Fab Light chain / type: protein_or_peptide / ID: 5
Details: Full sequence for the light chain of monoclonal antibody LX-2D6
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.864713 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAWALLLLTL LTQDTGSWAQ SALTQPASVS GSPGHSTTIS CTGTSNDVGS YTLVSWYQQR PGKAPKLMIY EVNKRPSGVS TRFSGSKSG NTASLTISGL QAEDEADYYC CSYAGSSIWL FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
MAWALLLLTL LTQDTGSWAQ SALTQPASVS GSPGHSTTIS CTGTSNDVGS YTLVSWYQQR PGKAPKLMIY EVNKRPSGVS TRFSGSKSG NTASLTISGL QAEDEADYYC CSYAGSSIWL FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHKSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 434 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.9 mg/mL
BufferpH: 7 / Component:
ConcentrationName
1.0 xDPBS
20.0 mMEDTA
/ Details: 1 x DPBS, 20 mM EDTA, pH 7.0
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
Details: Exact grid type was Quantifoil R2/1 Cu grids with 2 nm continous carbon layer. Product no. AGS174-1-2CL, Agar Scientific.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3 ul of sample blotted for 3.5 seconds with -10 blot force on FEI Vitrobot mark IV..
DetailsSample purified by sucrose density gradient ultracentrifugation. Concentrated sample mixed with Fab to form complex.

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Electron microscopy

MicroscopeTFS KRIOS
DetailsCalibrated pixel size was 0.7303 A/pix.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 12000 / Average exposure time: 1.79 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 190028
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Five independent 3D models. Generated in CryoSPARC using ab-initio reconstruction with icosahedral symmetry applied.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 105643
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Software - details: Ab-initio reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1) / Software - details: Homogeneous refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3.1) / Software - details: Heterogeneous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

1hxs

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico modelAlphaFold model for Fab
DetailsInitial 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

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

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