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- EMDB-56483: 6B5 (Fab) - Polio 3 (VLP) complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56483
Title6B5 (Fab) - Polio 3 (VLP) complex
Map dataUnsharpened map.
Sample
  • Virus: Poliovirus 3
    • Protein or peptide: Capsid proteins, VP1
    • Protein or peptide: Capsid proteins, VP0
    • Protein or peptide: Capsid proteins, VP3
    • Protein or peptide: 6B5 Fab Heavy chain
    • Protein or peptide: 6B5 Fab Light chain
  • Ligand: SPHINGOSINE
  • 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesPoliovirus 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.8 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: 6B5 (Fab) - Polio 3 (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_56483.png

Downloads & links

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Map

FileDownload / File: emd_56483.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-0.20747082 - 0.7433064
Average (Standard dev.)0.0015316827 (±0.031304255)
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_56483_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_56483_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_56483_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 : Poliovirus 3

EntireName: Poliovirus 3
Components
  • Virus: Poliovirus 3
    • Protein or peptide: Capsid proteins, VP1
    • Protein or peptide: Capsid proteins, VP0
    • Protein or peptide: Capsid proteins, VP3
    • Protein or peptide: 6B5 Fab Heavy chain
    • Protein or peptide: 6B5 Fab Light chain
  • Ligand: SPHINGOSINE
  • Ligand: water

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Supramolecule #1: Poliovirus 3

SupramoleculeName: Poliovirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Recombinantly expressed virus-like particle of poliovirus type 3 Saukett strain.
NCBI-ID: 12086 / Sci species name: Poliovirus 3 / Sci species strain: Saukett / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.85 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 proteins, VP1

MacromoleculeName: Capsid proteins, VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3 / Strain: Saukett
Molecular weightTheoretical: 33.562785 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GIEDLITEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLVPSDTVQ TRHVIQRRSR SESTIESFFA RGACVAIIE VDNEEPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MELTFVVTAN FTNTNNGHAL NQVYQIMYIP P GAPTPKSW ...String:
GIEDLITEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLVPSDTVQ TRHVIQRRSR SESTIESFFA RGACVAIIE VDNEEPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MELTFVVTAN FTNTNNGHAL NQVYQIMYIP P GAPTPKSW DDYTWQTSSN PSIFYTYGAA PARISVPYVG LANAYSHFYD GFAKVPLKTD ANDQIGDSLY SAMTVDDFGV LA IRVVNDH NPTKVTSKVR IYMKPKHVRV WCPRPPRAVP YYGPGVDYKD NLNPLSEKGL TTY

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid proteins, VP0

MacromoleculeName: Capsid proteins, VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3 / Strain: Saukett
Molecular weightTheoretical: 37.623023 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYKDSASNA ASKQDYSQDP SKFTEPLKDV LIKTAPALNS PNVEACGYSD RVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDMG L FGQNMYYH ...String:
MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYKDSASNA ASKQDYSQDP SKFTEPLKDV LIKTAPALNS PNVEACGYSD RVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDMG L FGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GEKGGKFYSQ FNRDTAVTSP KR EFCPVDY LLGCGVLLGN AFVYPHQIIN LRTNNSATIV LPYVNAMAID SMVKHNNWGI AILPLSPLDF AQESSVEIPI TVT IAPMCS EFNGLRNVTA PKFQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid proteins, VP3

MacromoleculeName: Capsid proteins, VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3 / Strain: Saukett
Molecular weightTheoretical: 26.3151 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVLNTPGS NQYLTSDNYQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLENT KRNTMDMYRV TLSDSADLSQ PILCFSLSP ASDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV ...String:
GLPVLNTPGS NQYLTSDNYQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLENT KRNTMDMYRV TLSDSADLSQ PILCFSLSP ASDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV PWISNVTYRQ TTQDSFTEGG YISMFYQTRI VVPLSTPKSM SMLGFVSACN DFSVRLLRDT THISQSALPQ

UniProtKB: Genome polyprotein

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Macromolecule #4: 6B5 Fab Heavy chain

MacromoleculeName: 6B5 Fab Heavy chain / type: protein_or_peptide / ID: 4
Details: Full sequence for the heavy chain of monoclonal antibody 6B5
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.752344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLSWIFL LAILKGFQCE VQLVESGGGL VQPGRSLRLS CEASGFNFDD YAMHWVRQAP GKGLEWVSGI SWSSSSRDYA DSVKGRFTI SRDNAKNSLY LHMNSLREED TALYYCAKDM SYYGSGGVLH YYYYGMDVWG QGTTVTVSSA STKGPSVFPL A PSSKSTSG ...String:
MELGLSWIFL LAILKGFQCE VQLVESGGGL VQPGRSLRLS CEASGFNFDD YAMHWVRQAP GKGLEWVSGI SWSSSSRDYA DSVKGRFTI SRDNAKNSLY LHMNSLREED TALYYCAKDM SYYGSGGVLH YYYYGMDVWG QGTTVTVSSA STKGPSVFPL A PSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NT KVDKRVE PKSCDKTHTC PPCPAPELLG GPSVFLFPPK PKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKT KPREEQ YNSTYRVVSV LTVLHQDWLN GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVYTLPPSR EEMTKNQVSL TCLV KGFYP SDIAVEWESN GQPENNYKTT PPVLDSDGSF FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

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Macromolecule #5: 6B5 Fab Light chain

MacromoleculeName: 6B5 Fab Light chain / type: protein_or_peptide / ID: 5
Details: Full sequence for the light chain of monoclonal antibody 6B5
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.929635 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAWALLFLTL LTQGTGSWAQ SALTQPASVS GSPGQSITIS CTGTSSDVGG YDYVSWYQQH PGKAPKVMIY DVSNRPSGVS NRFSGSKSG NTASLTISGL QAEDEAEYYC TSYTRSSTLV FGTGTKVTVL GQPKANPTVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
MAWALLFLTL LTQGTGSWAQ SALTQPASVS GSPGQSITIS CTGTSSDVGG YDYVSWYQQH PGKAPKVMIY DVSNRPSGVS NRFSGSKSG NTASLTISGL QAEDEAEYYC TSYTRSSTLV FGTGTKVTVL GQPKANPTVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADGSPV KAGVETTKPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #6: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / 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

Concentration0.8 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: 164829
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: 1.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 56545
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

1pvc

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-9u06:
6B5 (Fab) - Polio 3 (VLP) complex

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